Contacts of the helix formed by residues 1461 - 1469 (chain I) in PDB entry 3AOH
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 GLY1461 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1104I GLU* 4.0 29.3 + - - -
1106I VAL* 5.6 2.2 - - - +
1108I ARG* 5.2 2.2 - - - +
1460I ILE* 1.3 78.1 - - - +
1462I LEU* 1.3 70.9 + - - -
1463I LYS 3.5 1.8 - - - -
1464I GLU* 4.1 4.9 - - - -
1465I ASN* 3.4 22.7 + - - +
1473I PRO* 3.5 10.4 - - - +
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Residues in contact with LEU1462 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041H GLU* 2.7 42.8 - - + +
1103I HIS 3.7 16.8 + - - +
1104I GLU* 4.5 0.2 - - - +
1105I ILE 5.9 0.4 - - - +
1106I VAL* 4.4 10.5 - - + -
1220I ALA* 4.3 11.2 - - + -
1223I ILE* 3.7 16.6 - - + -
1461I GLY* 1.3 73.0 - - - -
1463I LYS* 1.3 67.9 + - - +
1465I ASN 3.6 0.5 + - - -
1466I VAL* 2.9 30.8 + - + +
1472I ILE* 3.4 26.2 - - + -
1473I PRO* 3.5 20.0 - - + -
1474I ALA* 3.9 17.0 - - + +
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Residues in contact with LYS1463 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618I LEU* 3.6 37.2 - - + +
1100I ASP* 4.7 9.5 + - - +
1103I HIS* 3.4 35.6 + - + +
1436I SER* 3.5 35.0 - - - +
1439I SER* 4.6 6.9 - - - +
1440I PHE* 3.5 28.5 - - + -
1461I GLY 3.5 0.4 - - - -
1462I LEU* 1.3 80.4 - - - +
1464I GLU* 1.3 70.7 + - + +
1466I VAL* 3.0 10.5 + - - +
1467I ILE* 3.2 17.1 + - + +
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Residues in contact with GLU1464 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104I GLU* 5.4 6.1 - - - +
1433I SER* 3.4 22.6 + - - -
1435I LEU* 3.6 28.5 - - + +
1436I SER* 4.4 10.8 - - - +
1457I ASP* 3.0 22.5 - - - +
1458I GLU 3.4 3.1 - - - +
1459I LEU* 3.8 1.5 - - - -
1460I ILE* 2.5 43.2 + - - +
1461I GLY* 3.7 10.6 - - - +
1463I LYS* 1.3 78.2 - - + +
1465I ASN* 1.3 63.0 + - - +
1466I VAL 3.0 5.9 + - - -
1467I ILE* 3.1 23.4 + - - +
1468I LEU* 3.5 11.6 - - + +
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Residues in contact with ASN1465 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459I LEU* 4.8 3.8 - - + -
1461I GLY 3.4 17.7 - - - +
1462I LEU 3.6 2.0 + - - +
1463I LYS 3.3 0.6 - - - -
1464I GLU* 1.3 79.9 - - + +
1466I VAL* 1.3 61.4 + - - +
1468I LEU* 3.1 19.4 + - + +
1469I GLY 3.4 1.4 + - - -
1470I ARG* 2.9 61.4 + - - +
1471I LEU 2.8 22.4 - - - +
1472I ILE* 5.0 1.3 - - - -
1473I PRO* 2.9 24.3 - - + +
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Residues in contact with VAL1466 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037H VAL* 5.4 4.5 - - + -
1041H GLU* 4.9 8.7 - - - +
1049H LEU* 4.8 6.1 - - + -
1053H LEU* 4.3 20.9 - - + +
617I ASN* 2.6 39.2 - - - +
618I LEU* 3.9 12.1 - - + +
1462I LEU 2.9 24.6 + - - +
1463I LYS* 3.0 6.9 + - - +
1464I GLU 3.0 0.2 + - - -
1465I ASN* 1.3 75.7 - - - +
1467I ILE* 1.3 60.8 + - - +
1468I LEU 3.0 1.6 - - - -
1469I GLY* 2.5 28.6 + - - -
1470I ARG 4.9 3.4 - - - +
1472I ILE* 4.6 16.4 - - + -
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Residues in contact with ILE1467 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084H SER* 3.6 17.5 + - - +
1085H PHE* 4.6 3.6 + - - -
1088H LEU* 3.9 26.9 - - + +
613I ARG 4.7 3.8 - - - +
614I PHE* 3.9 29.4 - - + +
617I ASN* 4.1 13.8 - - + +
618I LEU* 4.4 11.9 - - + -
1435I LEU* 4.2 23.3 - - + +
1439I SER* 4.0 20.9 - - - +
1463I LYS* 3.2 23.3 - - + +
1464I GLU* 3.1 15.5 + - - +
1466I VAL* 1.3 77.4 - - + +
1468I LEU* 1.3 61.9 + - - +
1469I GLY 3.3 0.5 + - - -
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Residues in contact with LEU1468 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082H PRO* 3.1 24.6 - - - +
1085H PHE* 3.2 50.8 - - + +
1088H LEU* 6.1 4.0 - - + -
8I VAL* 4.9 5.4 - - + -
1435I LEU* 3.3 24.0 - - + -
1459I LEU* 3.0 37.2 - - + -
1464I GLU 3.5 7.6 - - - +
1465I ASN* 3.1 35.4 - - - +
1466I VAL 3.0 0.2 - - - -
1467I ILE* 1.3 77.4 - - - +
1469I GLY* 1.3 58.2 + - - +
1470I ARG* 3.0 8.8 + - + +
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Residues in contact with GLY1469 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050H GLN* 2.6 30.1 + - - +
1053H LEU* 5.2 7.9 - - - +
1054H THR* 4.4 7.3 - - - +
1082H PRO* 3.4 22.7 - - - +
1084H SER* 4.9 0.9 - - - -
617I ASN* 5.0 3.8 - - - -
1466I VAL* 2.5 25.2 + - - -
1467I ILE 3.1 0.9 - - - -
1468I LEU* 1.3 72.5 - - - +
1470I ARG* 1.3 57.6 + - - +
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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
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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