Contacts of the helix formed by residues 1551 - 1566 (chain A) in PDB entry 5A31
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 ASN1551 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075A GLN* 4.8 2.5 - - - -
1510A HIS* 4.7 10.9 + - - -
1549A GLU* 3.6 2.3 - - - +
1550A MET* 1.3 80.3 - - - +
1552A TYR* 1.3 68.3 + - - +
1553A GLY* 3.5 4.7 - - - +
1554A PHE* 2.9 43.6 + - - +
1555A HIS* 3.2 14.2 + - - -
1592A PHE 4.9 1.6 + - - -
1593A PRO 3.1 26.9 + - - -
1594A ALA* 3.3 20.6 + - - +
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Residues in contact with TYR1552 (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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1075A GLN* 3.5 40.8 - - + +
1078A MET* 3.3 31.7 + - + +
1079A ALA* 3.6 13.2 - - + -
1135A ALA 5.0 1.7 + - - -
1138A HIS* 4.2 6.6 + - - -
1551A ASN* 1.3 74.2 - - - +
1553A GLY* 1.3 66.0 + - - +
1554A PHE 3.3 0.2 + - - -
1555A HIS* 3.4 2.5 + - - +
1556A LEU* 3.1 35.6 + - + +
1593A PRO* 3.9 12.3 - - + -
1594A ALA 4.4 0.2 + - - -
1595A HIS* 3.4 11.9 - - - -
1596A SER* 3.0 49.3 + - - +
1604A GLN* 2.8 33.8 + - - -
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Residues in contact with GLY1553 (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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1551A ASN* 3.2 3.8 - - - +
1552A TYR* 1.3 82.3 - - - +
1554A PHE* 1.3 61.8 + - - +
1556A LEU* 3.1 7.8 + - - +
1557A ALA* 3.1 20.4 + - - +
1592A PHE* 3.9 18.9 - - - +
1593A PRO* 3.3 33.1 + - - -
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Residues in contact with PHE1554 (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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1510A HIS* 3.8 30.7 - + - -
1513A GLU* 3.2 33.9 - - + -
1514A THR* 3.4 34.5 - - - -
1517A SER* 3.7 15.7 - - - +
1549A GLU 3.9 10.3 - - - -
1550A MET* 4.2 7.2 - - - -
1551A ASN* 2.9 27.3 + - - +
1553A GLY* 1.3 73.2 - - - +
1555A HIS* 1.3 68.5 + - - +
1557A ALA* 3.0 5.7 + - - +
1558A HIS* 2.9 42.2 + - + -
1592A PHE* 4.0 24.0 - + + -
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Residues in contact with HIS1555 (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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1072A GLN 4.6 4.9 - - - -
1075A GLN* 3.8 3.7 - - + +
1076A ARG* 3.4 51.0 + - + -
1079A ALA* 3.6 15.3 - - + -
1542A LEU 4.8 5.4 - - - -
1543A HIS* 4.9 1.1 - - - -
1546A THR* 3.6 31.6 + - - -
1550A MET* 3.8 29.9 + - + +
1551A ASN 3.2 11.1 + - - -
1552A TYR 3.5 7.4 - - - +
1554A PHE* 1.3 78.4 - - - +
1556A LEU* 1.3 64.0 + - - +
1558A HIS* 3.1 11.0 + - - +
1559A HIS* 3.0 32.4 + - + -
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Residues in contact with LEU1556 (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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1079A ALA* 3.1 16.5 - - + +
1082A VAL* 3.6 39.3 - - + -
1138A HIS* 5.0 1.3 - - - +
1552A TYR* 3.1 43.3 + - + +
1553A GLY 3.3 10.1 - - - +
1555A HIS* 1.3 78.3 - - - +
1557A ALA* 1.3 57.0 + - - +
1559A HIS* 3.4 1.4 + - - +
1560A MET* 2.8 47.0 + - + +
1592A PHE* 5.6 1.8 - - + -
1593A PRO* 4.7 14.4 - - + -
1604A GLN* 4.4 6.7 - - + +
1607A ARG* 4.3 10.3 - - + +
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Residues in contact with ALA1557 (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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1517A SER* 4.0 12.9 - - - +
1520A LEU* 5.5 0.2 - - - +
1521A LEU* 3.7 16.6 - - + +
1553A GLY 3.1 8.9 + - - +
1554A PHE 3.0 9.0 + - - +
1556A LEU* 1.3 79.4 - - - +
1558A HIS* 1.3 60.4 + - - +
1560A MET* 3.6 7.0 + - - -
1561A ALA* 3.2 15.8 + - - +
1592A PHE* 3.5 44.0 - - + -
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Residues in contact with HIS1558 (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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1513A GLU* 5.5 1.4 + - - +
1516A LEU* 4.8 6.4 - - + +
1517A SER* 3.6 23.7 + - - -
1520A LEU* 3.9 12.8 - - + -
1539A CYS* 4.1 11.0 - - - +
1542A LEU* 3.7 49.4 - - + +
1543A HIS* 4.8 1.5 + - - +
1550A MET* 3.7 31.3 - - + -
1554A PHE* 2.9 26.8 + - + +
1555A HIS* 3.7 12.6 - - - +
1557A ALA* 1.3 73.7 - - - +
1559A HIS* 1.3 68.4 + - + +
1561A ALA* 3.1 10.4 + - - +
1562A LEU* 3.0 24.4 + - - +
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Residues in contact with HIS1559 (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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1040A LEU 4.7 2.2 - - - -
1041A LEU* 4.3 11.4 - - + +
1076A ARG* 3.9 9.6 - - - +
1079A ALA* 4.1 20.2 - - + +
1080A LEU* 3.3 30.4 - - + +
1083A GLY* 3.9 13.2 - - - -
1543A HIS* 3.2 46.3 - + + +
1555A HIS* 3.0 38.2 + - + +
1556A LEU 3.8 3.1 - - - +
1558A HIS* 1.3 76.9 - - + +
1560A MET* 1.3 59.3 + - - +
1561A ALA 3.0 1.6 - - - -
1562A LEU* 2.7 17.1 + - + +
1563A GLY* 2.7 28.4 + - - -
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Residues in contact with MET1560 (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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1082A VAL* 3.9 13.7 - - + -
1083A GLY* 4.3 1.4 - - - -
1086A MET* 3.3 37.9 - - + +
1521A LEU* 3.9 10.0 - - + +
1556A LEU* 2.8 26.0 + - + +
1557A ALA* 3.7 6.5 - - - +
1559A HIS* 1.3 76.0 - - - +
1561A ALA* 1.3 61.5 + - - +
1564A LEU* 3.3 20.1 + - - +
1587A ALA 4.3 3.6 - - - +
1588A LEU* 3.8 27.1 - - + -
1592A PHE* 4.5 15.7 - - + -
1607A ARG* 3.5 52.3 - - + +
1610A TYR* 5.3 0.2 - - - -
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Residues in contact with ALA1561 (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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1520A LEU* 4.1 20.2 - - + +
1521A LEU* 3.6 14.5 - - + +
1524A ALA* 3.4 22.6 - - + +
1539A CYS* 3.9 15.3 - - - -
1557A ALA 3.2 11.7 + - - +
1558A HIS 3.1 11.8 + - - +
1559A HIS 3.0 0.6 - - - -
1560A MET* 1.3 73.7 - - - +
1562A LEU* 1.3 66.4 + - - +
1564A LEU* 3.1 10.1 + - - -
1565A LEU* 3.2 11.8 + - - +
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Residues in contact with LEU1562 (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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1037A VAL* 4.3 7.6 - - + -
1040A LEU* 3.6 26.7 - - + -
1041A LEU* 3.9 35.9 - - + -
1536A LEU* 4.3 12.8 - - + -
1539A CYS* 3.9 20.6 - - + -
1558A HIS 3.0 11.5 + - - +
1559A HIS* 2.7 17.8 + - - +
1561A ALA* 1.3 76.5 - - - +
1563A GLY* 1.3 61.8 + - - +
1565A LEU* 3.3 20.0 + - + +
1566A PHE* 3.4 33.8 + - + -
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Residues in contact with GLY1563 (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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1041A LEU* 5.3 1.4 - - - +
1083A GLY* 3.8 11.5 + - - -
1086A MET* 3.7 26.6 - - - +
1087A PHE* 4.4 7.2 - - - -
1559A HIS 2.7 16.8 + - - -
1560A MET 4.0 1.6 - - - -
1562A LEU* 1.3 73.1 - - - +
1564A LEU* 1.3 56.1 + - - +
1566A PHE 3.1 5.1 + - - -
1567A LEU* 2.8 29.6 + - - -
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Residues in contact with LEU1564 (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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1086A MET* 2.8 38.6 - - + -
1521A LEU* 4.3 12.8 - - + +
1524A ALA* 4.1 7.4 - - + -
1525A MET* 3.7 34.8 - - + +
1528A ALA* 3.3 9.9 - - + +
1529A GLY 2.9 20.7 + - - -
1560A MET 3.3 10.6 + - - +
1561A ALA 3.1 9.6 + - - +
1563A GLY* 1.3 74.6 - - - +
1565A LEU* 1.3 59.1 + - - +
1567A LEU* 3.3 18.0 + - + +
1574A LEU* 3.8 27.8 - - + -
1588A LEU* 5.0 11.2 - - + -
1610A TYR* 5.0 9.4 - - + -
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Residues in contact with LEU1565 (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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1524A ALA* 4.1 9.0 - - + -
1527A MET* 3.5 20.2 - - + +
1529A GLY 2.9 28.9 - - - +
1530A SER 4.6 0.2 - - - +
1531A GLY* 3.0 18.0 + - - -
1532A ASN 4.3 12.6 - - - +
1535A VAL* 3.6 47.6 - - + -
1536A LEU* 3.7 24.5 - - + +
1539A CYS* 4.3 4.7 - - - -
1561A ALA 3.2 10.1 + - - +
1562A LEU* 3.4 17.3 - - + +
1563A GLY 3.2 0.2 - - - -
1564A LEU* 1.3 77.7 - - - +
1566A PHE* 1.3 63.5 + - + +
1567A LEU 3.4 0.2 - - - -
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Residues in contact with PHE1566 (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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1028A TRP* 3.7 32.5 - + + -
1033A ARG* 4.5 13.5 - - + -
1034A VAL* 4.5 4.9 - - + -
1037A VAL* 3.2 36.3 - - + -
1087A PHE* 3.4 31.8 - + + +
1529A GLY 4.3 3.1 - - - -
1531A GLY* 3.3 29.4 - - - -
1536A LEU* 3.8 21.3 - - + -
1562A LEU* 3.4 27.1 + - + +
1563A GLY 3.1 7.5 + - - +
1565A LEU* 1.3 80.6 - - + +
1567A LEU* 1.3 65.6 + - - +
1568A GLY 3.1 0.9 + - - -
1569A GLY 3.1 13.0 + - - -
1570A GLY 4.0 3.8 - - - +
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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
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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