Contacts of the helix formed by residues 1486 - 1507 (chain A) in PDB entry 2H7C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1486 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451A TYR* 3.9 6.9 + - - -
1454A SER* 5.0 3.4 + - - -
1484A GLY 3.6 0.8 + - - -
1485A ALA* 1.3 78.5 - - - +
1487A GLU* 1.3 65.2 + - - +
1488A GLU* 3.6 6.5 + - - +
1489A GLU* 3.1 32.7 + - - +
1490A ILE* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485A ALA 3.8 1.0 + - - +
1486A SER* 1.3 74.1 - - - +
1488A GLU* 1.3 62.1 + - - +
1490A ILE* 3.3 24.9 + - - +
1491A ARG* 3.1 44.0 + - - +
1494A LYS* 5.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451A TYR* 3.2 34.0 + - + +
1486A SER* 3.2 8.1 + - - +
1487A GLU* 1.3 80.8 - - - +
1489A GLU* 1.3 56.4 + - - +
1491A ARG* 3.5 17.8 + - - +
1492A LEU* 3.1 26.0 + - + +
1531A ALA* 3.9 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451A TYR* 3.7 22.9 - - + +
1453A PRO* 3.2 10.0 - - - +
1454A SER* 2.6 51.4 + - - -
1455A PHE* 3.3 17.9 - - + -
1474A SER* 5.2 3.1 + - - +
1479A PRO* 3.7 11.0 - - + +
1485A ALA* 3.7 13.5 - - + +
1486A SER* 3.1 25.0 + - - +
1488A GLU* 1.3 76.5 - - - +
1490A ILE* 1.3 60.4 + - - +
1492A LEU* 3.4 7.3 + - + +
1493A SER* 3.1 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479A PRO* 3.9 30.7 - - + +
1480A PHE* 3.6 15.2 - - + -
1485A ALA* 4.0 14.4 - - + +
1486A SER 3.1 14.6 + - - +
1487A GLU* 3.6 29.8 - - - +
1488A GLU 3.3 0.2 - - - -
1489A GLU* 1.3 73.4 - - - +
1491A ARG* 1.3 65.1 + - - +
1493A SER 3.4 0.3 + - - -
1494A LYS* 3.1 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487A GLU* 3.1 31.3 + - - +
1488A GLU* 3.7 25.0 - - - +
1490A ILE* 1.3 80.2 - - - +
1492A LEU* 1.3 61.6 + - - +
1494A LYS* 3.5 10.9 + - - +
1495A MET* 3.2 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1449A PHE* 4.0 7.9 - - + -
1451A TYR* 3.6 46.0 - - + -
1474A SER* 3.7 20.4 - - - +
1488A GLU* 3.1 17.5 + - + +
1489A GLU* 3.6 5.4 - - + +
1491A ARG* 1.3 78.8 - - - +
1493A SER* 1.3 56.7 + - - +
1495A MET* 3.3 13.1 + - + +
1496A VAL* 2.9 35.9 + - + +
1529A ILE* 3.9 24.7 - - + -
1530A GLY 3.9 22.4 - - - +
1531A ALA* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474A SER* 2.7 35.8 + - - +
1477A GLY* 3.2 19.6 - - - -
1479A PRO* 3.9 12.6 - - - -
1480A PHE* 3.6 15.4 - - - -
1489A GLU 3.1 16.8 + - - -
1490A ILE 3.8 0.9 - - - -
1491A ARG 3.4 0.4 - - - -
1492A LEU* 1.3 74.9 - - - +
1494A LYS* 1.3 65.8 + - - +
1496A VAL 3.3 0.7 + - - -
1497A MET* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160A HIS* 5.2 8.3 - - - +
1161A GLU* 4.6 1.2 - - - +
1480A PHE* 3.3 21.5 - - + -
1487A GLU* 5.5 2.8 + - - -
1490A ILE* 3.1 43.3 + - + +
1491A ARG* 3.7 8.7 - - - +
1493A SER* 1.3 75.0 - - - +
1495A MET* 1.3 63.8 + - - +
1497A MET* 4.0 9.5 - - - +
1498A LYS* 3.1 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491A ARG* 3.2 11.9 + - + +
1492A LEU* 3.6 17.3 - - + +
1494A LYS* 1.3 79.7 - - - +
1496A VAL* 1.3 61.5 + - + +
1498A LYS* 3.3 3.6 - - - +
1499A PHE* 3.0 55.5 + - + -
1514A LEU* 3.7 20.0 - - + -
1515A PRO* 3.9 20.4 - - + -
1529A ILE* 3.8 22.0 - - + -
1533A THR* 3.4 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1449A PHE* 4.7 4.0 - - + -
1471A GLU* 6.4 0.4 - - + -
1474A SER* 3.9 16.8 - - - -
1475A VAL* 3.6 38.6 - - + +
1492A LEU* 2.9 34.6 + - + +
1493A SER 3.8 3.1 - - - +
1495A MET* 1.3 76.6 - - + +
1497A MET* 1.3 67.0 + - - +
1499A PHE* 3.2 7.4 + - - -
1500A TRP* 2.9 39.6 + - + +
1529A ILE* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156A ALA 4.2 0.2 - - - +
1157A LEU* 3.8 37.4 - - + +
1160A HIS* 3.8 24.9 - - + +
1161A GLU* 3.5 9.1 - - + +
1474A SER 3.4 12.8 - - - +
1475A VAL 3.5 9.6 - - - +
1477A GLY* 3.8 19.3 - - - -
1480A PHE* 3.5 36.8 - - + -
1493A SER* 2.9 20.2 + - - +
1494A LYS* 4.0 6.5 - - - +
1496A VAL* 1.3 75.8 - - - +
1498A LYS* 1.3 57.7 + - - +
1500A TRP* 3.7 5.6 - - - +
1501A ALA* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160A HIS 5.0 2.6 + - - -
1161A GLU* 3.1 32.3 + - - +
1494A LYS* 3.1 16.4 + - + +
1495A MET 3.3 9.6 - - - +
1497A MET* 1.3 76.7 - - - +
1499A PHE* 1.3 53.3 + - - +
1501A ALA* 3.4 0.7 + - - +
1502A ASN* 2.8 51.1 + - - +
1505A ARG* 5.0 0.7 - - - +
1512A GLU 5.2 8.7 - - - +
1514A LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347A MET* 5.0 0.2 - - - -
1495A MET* 3.0 45.9 + - + -
1496A VAL* 3.5 8.7 - - - +
1498A LYS* 1.3 79.2 - - - +
1500A TRP* 1.3 69.0 + - + +
1502A ASN* 3.3 1.7 + - - +
1503A PHE* 2.9 30.2 + - - +
1509A PRO* 3.3 25.5 - - - +
1510A ASN* 4.7 2.2 - - - -
1514A LEU* 3.6 24.7 - - + -
1515A PRO* 3.4 32.5 - - + -
1517A TRP* 3.8 33.4 - + + -
1527A LEU* 3.6 25.4 - - + -
1529A ILE* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136A MET* 3.9 14.0 - - + +
1157A LEU* 5.5 3.4 - - + -
1218A PHE* 4.0 8.7 - + - -
1244A ILE* 3.7 21.9 - - + +
1246A GLU* 3.0 24.3 + - + -
1347A MET* 3.9 15.0 - - - -
1447A TYR* 3.6 43.5 - + - -
1449A PHE* 6.5 0.7 - + - -
1471A GLU* 5.4 1.6 - - + -
1475A VAL* 3.6 34.2 - - + +
1496A VAL* 2.9 46.6 + - + +
1497A MET* 3.7 6.3 - - - +
1499A PHE* 1.3 83.8 - - + +
1501A ALA* 1.3 56.6 + - - +
1503A PHE* 3.2 9.0 + - - +
1504A ALA* 2.9 25.6 + - - +
1517A TRP* 4.0 20.4 - + - -
1529A ILE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136A MET* 4.4 6.3 - - - -
1157A LEU* 5.1 1.1 - - + +
1161A GLU* 3.3 35.2 - - + +
1163A VAL* 4.1 8.0 - - + +
1497A MET 2.8 17.0 + - - +
1500A TRP* 1.3 68.7 - - - +
1502A ASN* 1.3 63.0 + - - +
1504A ALA* 3.1 9.7 + - - +
1505A ARG* 2.8 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1498A LYS* 2.8 29.5 + - - +
1499A PHE 3.6 0.2 - - - +
1501A ALA* 1.3 71.3 - - - +
1503A PHE* 1.3 58.7 + - - +
1505A ARG* 2.9 29.9 + - - +
1506A ASN* 2.8 33.7 + - - +
1508A ASN 3.2 9.1 - - - +
1509A PRO 3.1 30.4 + - - +
1510A ASN 3.4 13.6 + - - +
1511A GLY* 3.8 5.8 - - - -
1514A LEU* 3.3 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216A THR* 4.6 0.9 - - + -
1242A ARG* 3.7 21.0 - - + +
1243A ALA 3.3 18.8 - - - -
1244A ILE* 3.7 23.6 - - + -
1345A PRO* 3.6 30.5 - - + -
1346A TYR 4.4 0.2 - - - -
1347A MET* 3.6 29.2 - - + -
1445A TYR* 3.9 16.2 - + - -
1499A PHE 2.9 14.0 + - - +
1500A TRP* 3.3 9.0 - - - +
1502A ASN* 1.3 77.5 - - - +
1504A ALA* 1.3 59.6 + - - +
1507A GLY* 2.7 56.8 + - - -
1508A ASN 3.5 8.4 + - - -
1509A PRO* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134A PRO* 4.4 13.8 - - + +
1135A VAL 5.2 0.4 - - - +
1136A MET* 3.9 27.4 - - + -
1163A VAL* 5.1 0.2 - - + -
1214A SER* 3.5 10.6 + - - -
1216A THR* 3.3 26.2 + - + +
1242A ARG* 2.8 23.4 + - - -
1500A TRP 2.9 13.6 + - - +
1501A ALA* 3.1 8.5 + - - +
1503A PHE* 1.3 76.2 - - - +
1505A ARG* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134A PRO* 3.8 23.9 - - + +
1161A GLU* 2.9 49.5 + - - -
1162A ASN* 4.5 3.2 + - - +
1163A VAL* 4.0 5.3 - - - +
1214A SER* 4.7 3.7 + - - -
1242A ARG* 3.0 13.2 + - - -
1498A LYS* 5.0 1.2 - - - +
1501A ALA* 2.8 28.8 + - - +
1502A ASN* 2.9 31.1 + - - +
1504A ALA* 1.3 77.9 - - - +
1506A ASN* 1.3 76.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242A ARG* 3.5 10.7 + - - +
1345A PRO* 5.4 0.2 - - - +
1502A ASN* 2.8 23.4 + - - +
1505A ARG* 1.3 92.3 - - - +
1507A GLY* 1.3 59.8 + - - +
1508A ASN* 3.0 20.3 + - + +
1510A ASN 5.0 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242A ARG* 3.7 8.8 - - - +
1345A PRO* 3.8 31.9 - - - +
1443A PRO* 4.1 6.8 - - - +
1445A TYR* 3.5 16.5 + - - -
1503A PHE* 2.7 35.2 + - - -
1506A ASN* 1.3 72.6 - - - +
1508A ASN* 1.3 57.5 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il