Contacts of the helix formed by residues 1495 - 1516 (chain A) in PDB entry 2REA
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 HIS1495 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493A ARG 4.8 0.7 - - - -
1494A THR* 1.4 83.2 + - - +
1496A ILE* 1.3 68.7 + - - +
1497A LYS 3.9 0.7 - - - -
1498A ASP* 3.1 26.3 + - + +
1499A VAL* 3.2 15.8 + - - +
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Residues in contact with ILE1496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434A LYS* 6.1 4.7 - - - -
1442A TYR* 4.1 16.7 - - + +
1495A HIS* 1.3 72.3 - - - +
1497A LYS* 1.3 62.7 + - - +
1499A VAL* 3.1 11.7 + - - +
1500A ALA 3.4 8.3 + - - -
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Residues in contact with LYS1497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432A TYR* 4.1 12.3 + - + +
1442A TYR* 3.4 20.8 + - + +
1495A HIS 3.9 0.2 - - - -
1496A ILE* 1.3 77.9 - - - +
1498A ASP* 1.3 62.2 - - - +
1500A ALA* 3.4 3.2 - - - +
1501A ALA* 3.0 28.4 + - + +
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Residues in contact with ASP1498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1494A THR* 3.5 13.4 - - - -
1495A HIS* 3.1 33.4 + - + +
1497A LYS* 1.3 84.7 - - - +
1499A VAL* 1.3 59.8 + - - +
1501A ALA* 3.3 7.4 + - - +
1502A LYS* 3.2 25.6 + - - +
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Residues in contact with VAL1499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488A ARG* 5.8 4.3 - - + -
1491A LEU* 6.3 1.6 - - + +
1494A THR* 4.7 9.2 - - - +
1495A HIS 3.2 22.0 + - - +
1496A ILE* 3.1 8.8 + - - +
1498A ASP* 1.3 75.4 - - - +
1500A ALA* 1.3 68.6 + - - +
1501A ALA 3.1 1.3 - - - -
1502A LYS* 3.0 22.6 + - + +
1503A ARG* 2.8 63.6 + - + +
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Residues in contact with ALA1500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432A TYR* 3.7 25.0 - - + -
1442A TYR* 3.5 42.3 - - + -
1444A TYR* 3.4 16.1 - - - +
1496A ILE 3.4 5.5 + - - -
1497A LYS 3.4 9.4 - - - +
1499A VAL* 1.3 77.7 - - - +
1501A ALA* 1.3 62.0 + - - +
1503A ARG* 3.3 2.3 + - - +
1504A LYS 3.0 19.4 + - - -
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Residues in contact with ALA1501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432A TYR* 3.4 21.7 + - - +
1497A LYS* 3.0 16.2 + - + +
1498A ASP* 3.7 8.1 - - - +
1499A VAL 3.1 0.6 - - - -
1500A ALA* 1.3 78.0 - - - +
1502A LYS* 1.3 57.3 + - - +
1504A LYS* 3.9 8.6 + - - +
1505A ILE* 3.5 20.1 - - - +
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Residues in contact with LYS1502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488A ARG* 2.9 57.7 - - - +
1491A LEU* 4.8 9.9 - - - +
1498A ASP* 3.2 12.5 + - - +
1499A VAL* 3.0 28.6 + - + +
1501A ALA* 1.3 74.2 - - - +
1503A ARG* 1.3 67.6 + - + +
1504A LYS 3.3 0.4 - - - -
1505A ILE* 3.3 10.8 + - - +
1506A GLU* 3.0 49.3 + - - +
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Residues in contact with ARG1503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1444A TYR* 3.4 32.5 + - + +
1463A PHE* 3.6 62.9 - - + +
1486A PRO 5.4 0.6 + - - -
1487A ASN* 6.1 1.4 - - - +
1488A ARG* 5.3 9.3 + - - +
1499A VAL* 2.8 39.0 + - - +
1500A ALA 3.7 0.4 - - - +
1502A LYS* 1.3 81.9 - - + +
1504A LYS* 1.3 65.0 + - - +
1505A ILE 3.0 1.8 - - - -
1506A GLU* 4.2 11.2 - - - +
1507A LEU* 2.8 37.3 + - + +
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Residues in contact with LYS1504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429A VAL* 3.8 31.9 - - + +
1430A PHE 2.9 28.5 + - - -
1431A THR* 3.5 16.1 + - - +
1432A TYR* 3.9 32.4 - - + -
1444A TYR* 4.1 7.1 - - - -
1500A ALA 3.0 9.1 + - - +
1501A ALA 4.0 7.4 - - - +
1502A LYS 3.3 0.6 - - - -
1503A ARG* 1.3 73.3 - - - +
1505A ILE* 1.3 64.4 + - + +
1508A ASN* 3.0 30.0 + - + +
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Residues in contact with ILE1505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1501A ALA 3.5 20.6 - - - +
1502A LYS* 3.3 10.5 + - - +
1503A ARG 3.0 0.4 - - - -
1504A LYS* 1.3 84.5 - - + +
1506A GLU* 1.3 64.0 + - + +
1508A ASN* 3.3 5.8 + - - +
1509A SER* 2.9 38.8 + - - +
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Residues in contact with GLU1506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486A PRO* 3.3 38.6 - - + +
1488A ARG* 3.4 29.8 + - - -
1502A LYS* 3.0 40.9 + - + +
1503A ARG* 4.1 9.3 - - - +
1505A ILE* 1.3 77.2 - - + +
1507A LEU* 1.3 61.0 + - - +
1509A SER* 3.3 5.7 + - - -
1510A TYR* 2.9 28.1 + - - +
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Residues in contact with LEU1507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429A VAL* 3.9 13.9 - - + -
1444A TYR* 3.8 39.9 - - + -
1463A PHE* 4.0 25.1 - - + -
1466A PHE* 4.0 39.9 - - + -
1485A PHE* 4.5 4.7 - - + -
1486A PRO* 4.1 16.6 - - + -
1503A ARG* 2.8 30.9 + - + +
1504A LYS* 5.1 0.2 - - - -
1506A GLU* 1.3 68.3 - - - +
1508A ASN* 1.3 66.6 + - - +
1510A TYR* 3.2 5.7 + - + +
1511A LEU* 3.0 25.8 + - - +
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Residues in contact with ASN1508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428A SER* 3.1 11.2 - - - +
1429A VAL* 3.1 39.5 - - + +
1504A LYS 3.0 21.0 + - - +
1505A ILE* 3.6 5.8 - - - +
1506A GLU 3.2 0.2 - - - -
1507A LEU* 1.3 78.9 - - - +
1509A SER* 1.3 58.2 + - - +
1511A LEU* 3.3 2.5 + - - +
1512A GLN* 2.9 64.0 + - - +
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Residues in contact with SER1509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505A ILE* 2.9 23.5 + - - +
1506A GLU* 3.8 5.6 - - - -
1508A ASN* 1.3 74.9 + - - +
1510A TYR* 1.3 67.8 + - - +
1512A GLN* 4.0 9.0 - - - +
1513A SER* 2.9 28.3 + - - -
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Residues in contact with TYR1510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1466A PHE* 4.6 9.9 - + - -
1469A LEU* 4.7 9.0 - - + -
1470A HIS* 2.6 44.2 - + + +
1473A LEU* 4.1 11.6 - - - +
1483A PRO* 3.6 26.4 - - + +
1484A GLY 3.4 21.1 - - - +
1485A PHE* 3.8 28.0 - + - -
1486A PRO* 4.4 5.4 - - + -
1506A GLU 2.9 14.3 + - - +
1507A LEU* 3.3 13.5 - - + +
1509A SER* 1.3 75.7 - - - +
1511A LEU* 1.3 62.8 + - + +
1513A SER* 2.9 6.9 + - - -
1514A LEU* 2.6 61.3 + - + +
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Residues in contact with LEU1511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427A VAL* 3.7 34.5 - - + -
1429A VAL* 4.0 25.4 - - + +
1446A VAL* 4.0 11.4 - - + -
1466A PHE* 3.6 27.1 - - + -
1469A LEU* 5.6 0.2 - - + -
1507A LEU 3.0 11.9 + - - +
1508A ASN* 3.4 8.1 - - - +
1510A TYR* 1.3 86.9 - - + +
1512A GLN* 1.4 64.2 + - - +
1514A LEU* 3.8 13.9 - - + +
1515A MET* 3.1 29.3 + - - +
1530A PHE* 4.6 3.8 - - + -
1531A PHE* 4.3 13.5 - - + -
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Residues in contact with GLN1512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426A GLU* 5.9 2.0 - - - +
1427A VAL* 2.9 35.8 + - - +
1428A SER* 5.5 0.4 - - - -
1508A ASN* 2.9 53.1 + - - +
1509A SER* 3.3 8.0 + - - +
1511A LEU* 1.4 71.3 - - - +
1513A SER* 1.3 64.1 + - - +
1515A MET* 4.0 2.0 - - - +
1516A ASN* 3.2 38.4 + - - +
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Residues in contact with SER1513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483A PRO* 3.7 25.1 - - - +
1509A SER* 2.9 17.0 + - - -
1510A TYR 3.4 6.5 - - - -
1512A GLN* 1.3 79.3 - - - +
1514A LEU* 1.3 63.4 + - - +
1515A MET 3.2 0.9 + - - -
1516A ASN* 3.4 3.0 + - - -
1517A ALA* 3.2 19.4 + - - +
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Residues in contact with LEU1514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469A LEU* 4.0 20.9 - - + -
1473A LEU* 3.7 18.4 - - + -
1483A PRO* 3.4 20.8 - - + +
1510A TYR* 2.6 44.3 + - + +
1511A LEU* 3.8 14.6 - - + +
1513A SER* 1.3 73.4 - - - +
1515A MET* 1.3 63.6 + - + +
1517A ALA* 2.8 24.8 - - - +
1521A VAL* 3.7 23.1 - - + -
1522A ALA* 3.9 7.6 - - - -
1527A VAL* 4.0 16.4 - - + -
1531A PHE* 5.4 1.1 - - + -
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Residues in contact with MET1515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1421A ASP* 3.5 23.3 + - - +
1424A ILE* 3.4 36.1 - - + -
1427A VAL* 3.9 17.3 - - + +
1511A LEU* 3.1 19.8 + - - +
1512A GLN* 4.2 3.1 - - - +
1514A LEU* 1.3 79.4 - - + +
1516A ASN* 1.3 68.2 + - - +
1517A ALA 3.3 4.9 - - - +
1522A ALA* 4.1 24.4 - - - +
1527A VAL* 4.1 12.3 - - + -
1531A PHE* 3.8 29.2 - - + -
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Residues in contact with ASN1516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512A GLN* 3.2 28.7 + - - +
1513A SER* 3.8 4.3 - - - +
1515A MET* 1.3 85.3 + - - +
1517A ALA* 1.3 63.0 + - - +
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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
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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) + - + + + + + -
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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