Contacts of the helix formed by residues 1504 - 1523 (chain A) in PDB entry 5XJY
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 ASN1504 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU 4.9 4.3 - - - +
91A PRO* 5.0 3.8 - - - +
1457A GLN* 3.3 24.6 + - - +
1458A ASN 4.2 1.2 + - - -
1460A SER* 4.8 16.9 - - - +
1503A ARG* 1.3 73.9 - - - +
1505A ILE* 1.3 65.7 + - - +
1506A SER* 3.4 5.2 + - - -
1507A ASP* 3.4 8.4 + - + +
1508A TYR* 3.1 21.7 + - - +
1B NAG 1.4 73.1 + - + +
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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
----------------------------------------------------------
89A GLU 5.5 1.9 + - - +
90A ALA 5.2 1.5 - - - +
91A PRO* 4.8 20.8 - - + +
1390A PHE* 3.9 21.1 - - + -
1392A SER* 3.4 28.3 - - - +
1394A ASP* 5.7 0.2 - - - +
1500A LEU* 3.8 29.4 - - + -
1502A GLY* 6.2 0.2 - - - -
1503A ARG 3.1 17.4 + - - +
1504A ASN* 1.3 73.2 + - - +
1506A SER* 1.3 63.4 + - - +
1508A TYR* 3.4 1.4 + - - +
1509A LEU* 3.0 31.2 + - + +
1536A SER* 3.6 18.2 - - - +
1593A TRP* 4.4 17.0 - - + -
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Residues in contact with SER1506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 4.1 15.7 + - - -
85A PRO* 4.2 10.8 - - - +
89A GLU* 4.1 39.2 + - - -
623A PRO* 4.0 8.8 - - - +
1504A ASN* 3.4 7.9 + - - -
1505A ILE* 1.3 78.7 - - - +
1507A ASP* 1.3 63.2 + - - +
1509A LEU* 3.3 6.2 + - - +
1510A VAL* 3.0 32.6 + - - +
1593A TRP* 4.9 4.2 - - - -
1B NAG 4.2 5.4 - - - -
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Residues in contact with ASP1507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 5.1 2.1 - - - +
55A HIS* 6.0 0.2 - - - -
1459A PRO* 5.2 1.0 - - - +
1460A SER 4.7 0.5 + - - -
1461A PRO* 3.2 28.2 - - + +
1483A GLY* 5.2 2.6 + - - -
1504A ASN* 3.4 10.8 + - + +
1506A SER* 1.3 79.2 + - - +
1508A TYR* 1.3 66.9 + - - +
1510A VAL* 4.5 5.7 - - - +
1511A LYS* 2.4 56.6 + - - +
1B NAG 3.3 37.5 - - - +
2B NAG 5.5 0.7 - - - +
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Residues in contact with TYR1508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483A GLY* 3.8 32.0 - - - -
1485A PRO 4.5 0.7 - - - -
1487A PRO* 3.5 24.4 - - + +
1498A GLN* 2.7 37.4 + - - -
1500A LEU* 3.5 40.2 - - + -
1503A ARG* 3.9 19.7 - - + +
1504A ASN 3.1 14.5 + - - +
1505A ILE 3.6 7.9 - - - +
1507A ASP* 1.3 77.0 - - - +
1509A LEU* 1.3 68.6 + - + +
1512A THR* 2.9 59.6 + - + +
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Residues in contact with LEU1509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A MET* 3.8 25.6 - - + -
623A PRO* 4.4 13.1 - - + +
1390A PHE* 3.6 35.4 - - + -
1505A ILE* 3.0 26.6 + - + +
1506A SER 3.7 3.6 - - - +
1507A ASP 3.3 0.2 - - - -
1508A TYR* 1.3 83.4 - - + +
1510A VAL* 1.3 68.0 + - - +
1513A TYR* 3.0 13.2 + - - +
1531A ARG* 3.0 48.3 + - - +
1593A TRP* 4.0 19.1 - - + -
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Residues in contact with VAL1510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 3.3 31.9 - - + +
55A HIS* 4.5 2.0 - - - +
623A PRO* 3.7 34.5 - - + +
624A TYR 4.8 0.2 - - - +
625A PRO* 3.7 26.8 - - + +
1464A GLN* 4.2 12.8 - - - +
1506A SER 3.0 17.8 + - - +
1507A ASP* 4.0 6.5 - - - +
1509A LEU* 1.3 77.8 - - - +
1511A LYS* 1.3 69.8 + - + +
1513A TYR* 3.8 2.7 - - - +
1514A VAL* 3.1 26.5 + - - +
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Residues in contact with LYS1511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 5.0 4.9 + - - -
1461A PRO* 4.0 4.5 - - + +
1462A ALA 4.0 18.3 + - - -
1463A CYS* 4.0 4.5 - - - +
1464A GLN* 3.6 45.5 + - + +
1478A PRO* 5.1 9.5 - - + +
1482A GLY* 3.4 35.9 - - - +
1507A ASP* 2.4 56.5 + - - +
1508A TYR 4.4 0.2 - - - +
1510A VAL* 1.3 81.6 - - + +
1512A THR* 1.3 60.9 + - - +
1514A VAL* 3.0 21.9 + - + +
1515A GLN* 3.0 14.8 + - - +
1B NAG 5.8 0.2 - - - -
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Residues in contact with THR1512 (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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1482A GLY 4.5 7.2 - - - -
1483A GLY 5.3 0.8 + - - -
1498A GLN* 5.1 0.7 - - - +
1508A TYR* 2.9 56.3 + - + +
1511A LYS* 1.3 78.8 - - - +
1513A TYR* 1.3 63.9 + - - +
1515A GLN* 3.7 20.3 + - - +
1516A ILE* 3.1 33.2 + - + +
1530A PHE* 5.7 2.0 - - + -
1531A ARG* 3.7 23.1 + - - +
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Residues in contact with TYR1513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TRP* 4.2 12.1 - - - -
623A PRO 5.8 1.6 - - - +
624A TYR* 3.5 39.1 + + - -
625A PRO* 4.2 22.2 - - + -
1475A PRO* 6.3 2.9 - - + -
1509A LEU 3.0 22.6 + - - +
1510A VAL 3.8 0.9 - - - +
1512A THR* 1.3 77.9 - - - +
1514A VAL* 1.3 67.1 + - - +
1516A ILE* 4.0 1.7 - - - -
1517A ILE* 3.1 49.1 + - + +
1529A GLU* 4.2 25.7 + - + +
1530A PHE* 5.0 13.9 - - + -
1531A ARG* 3.4 19.3 - - + +
1595A ASN* 5.2 8.1 - - - -
1597A LYS* 4.8 2.1 + - - -
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Residues in contact with VAL1514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A PRO* 3.6 28.5 - - + -
1464A GLN* 4.6 4.9 - - - +
1475A PRO* 4.9 9.0 - - + +
1476A VAL 3.1 36.8 - - - +
1477A CYS* 4.0 1.6 - - - -
1478A PRO* 3.7 20.2 - - + -
1510A VAL 3.1 16.7 + - - +
1511A LYS* 3.0 12.1 + - + +
1513A TYR* 1.3 78.8 - - - +
1515A GLN* 1.3 60.9 + - - +
1517A ILE* 3.1 4.7 + - - +
1518A ALA* 2.8 31.7 + - + +
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Residues in contact with GLN1515 (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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1478A PRO* 3.9 25.4 - - + +
1480A GLY 4.5 2.4 - - - +
1481A ALA* 4.2 12.3 - - - +
1482A GLY 4.1 18.6 + - - +
1483A GLY 5.6 1.8 + - - -
1484A LEU* 5.6 3.2 + - - +
1511A LYS 3.0 11.4 + - - +
1512A THR* 3.7 26.0 + - - +
1514A VAL* 1.3 79.5 - - - +
1516A ILE* 1.3 73.1 + - + +
1518A ALA* 4.5 4.0 - - - +
1519A LYS* 3.0 28.5 + - - +
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Residues in contact with ILE1516 (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 THR* 3.1 26.0 + - - +
1513A TYR 4.4 1.3 - - - +
1514A VAL 3.2 0.2 - - - -
1515A GLN* 1.3 90.5 - - + +
1517A ILE* 1.3 66.3 + - + +
1519A LYS* 3.8 22.7 - - + +
1520A SER* 3.0 26.2 + - - -
1527A VAL* 5.6 0.2 - - - +
1530A PHE* 3.5 59.0 - - + -
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Residues in contact with ILE1517 (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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574A TRP* 4.2 24.5 - - + -
1475A PRO* 4.8 13.5 - - + -
1513A TYR* 3.1 55.0 + - + +
1514A VAL* 3.8 2.9 - - - +
1516A ILE* 1.3 77.1 - - + +
1518A ALA* 1.3 60.8 + - - +
1520A SER 3.1 3.5 + - - -
1521A LEU* 2.9 42.9 + - + +
1527A VAL* 3.8 19.0 - - + +
1528A ASN 3.7 23.1 - - - +
1529A GLU* 5.1 1.3 - - + -
1530A PHE* 5.5 4.9 - - + +
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Residues in contact with ALA1518 (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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800A GLN* 6.2 2.0 - - - +
1475A PRO* 5.0 11.7 - - + -
1477A CYS* 5.8 7.6 - - + -
1514A VAL* 2.8 26.6 + - + +
1515A GLN* 4.7 3.4 - - - +
1517A ILE* 1.3 75.0 - - - +
1519A LYS* 1.3 63.1 + - - +
1521A LEU* 4.3 8.5 - - - +
1522A LYS* 3.3 30.6 + - - +
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Residues in contact with LYS1519 (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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1515A GLN 3.0 23.1 + - - +
1516A ILE* 3.8 22.9 - - + +
1518A ALA* 1.3 78.8 - - - +
1520A SER* 1.3 62.6 + - - +
1521A LEU 3.0 5.4 + - - -
1522A LYS* 3.5 11.5 + - - +
1523A ASN* 3.8 8.8 + - - +
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Residues in contact with SER1520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516A ILE* 3.0 19.0 + - - -
1517A ILE 3.4 3.6 - - - -
1519A LYS* 1.3 80.8 - - - +
1521A LEU* 1.3 56.4 + - - +
1523A ASN* 4.4 6.1 - - - -
1524A LYS 4.0 9.9 + - - -
1525A ILE* 4.0 23.0 + - - +
1527A VAL* 3.4 38.9 + - - +
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Residues in contact with LEU1521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TRP* 4.5 14.6 - - + -
638A ARG* 5.4 2.2 - - - +
796A LEU* 3.3 28.9 - - + +
799A GLU* 6.1 0.7 - - - +
800A GLN* 5.1 12.3 - - - +
1474A LEU* 4.9 18.6 - - + -
1475A PRO* 5.2 7.9 - - + -
1517A ILE* 2.9 29.0 + - + +
1518A ALA* 4.3 6.7 - - - -
1519A LYS 3.0 0.4 + - - -
1520A SER* 1.3 78.3 - - - +
1522A LYS* 1.3 63.4 + - - +
1523A ASN 3.3 1.1 - - - -
1524A LYS* 3.0 43.4 + - + +
1527A VAL* 4.5 13.7 - - + +
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Residues in contact with LYS1522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A LEU* 5.1 10.4 - - + +
797A PHE* 3.6 48.3 - - + -
800A GLN* 3.4 44.1 + - - +
1518A ALA* 3.3 20.6 + - - +
1519A LYS* 3.5 6.7 + - - +
1521A LEU* 1.3 78.1 - - - +
1523A ASN* 1.3 61.4 + - - +
1524A LYS* 3.4 3.5 + - - +
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Residues in contact with ASN1523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1519A LYS 3.8 10.6 + - - +
1520A SER* 4.7 5.6 - - - -
1521A LEU 3.3 0.2 - - - -
1522A LYS* 1.3 79.8 - - - +
1524A LYS* 1.3 68.0 + - - +
1525A ILE* 4.2 26.6 - - + +
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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
------------------------------------------------------------
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