Contacts of the helix formed by residues 1136 - 1146 (chain D) in PDB entry 6AH0
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 PRO1136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1134D LYS 3.9 1.6 - - - -
1135D LEU* 1.3 73.4 - - - +
1137D GLU* 1.3 63.4 + - - +
1138D GLU 3.4 2.2 - - - -
1139D VAL* 3.6 5.8 + - - +
1140D VAL* 3.4 16.8 + - - -
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Residues in contact with GLU1137 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135D LEU 3.8 2.2 + - - -
1136D PRO* 1.3 71.0 - - - +
1138D GLU* 1.3 59.7 + - - +
1140D VAL* 3.3 1.8 + - - +
1141D LYS* 2.9 26.7 + - - -
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Residues in contact with GLU1138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136D PRO 3.4 0.4 - - - -
1137D GLU* 1.3 76.4 - - - +
1139D VAL* 1.3 56.8 + - - +
1141D LYS* 3.6 1.9 + - - +
1142D LYS* 2.9 24.8 + - - -
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Residues in contact with VAL1139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136D PRO* 3.6 7.7 + - - +
1137D GLU 3.2 0.6 - - - -
1138D GLU* 1.3 74.3 - - - +
1140D VAL* 1.3 64.5 + - - +
1142D LYS* 3.0 3.4 + - - +
1143D ILE* 2.9 20.1 + - - -
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Residues in contact with VAL1140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136D PRO 3.4 10.8 + - - -
1137D GLU* 3.3 5.7 + - - +
1139D VAL* 1.3 74.2 - - - +
1141D LYS* 1.3 63.0 + - - +
1143D ILE* 3.1 4.6 + - - +
1144D GLU* 3.0 19.6 + - - -
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Residues in contact with LYS1141 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1137D GLU 2.9 16.7 + - - -
1138D GLU* 3.8 2.0 - - - +
1140D VAL* 1.3 74.4 - - - +
1142D LYS* 1.3 56.6 + - - +
1144D GLU* 3.2 3.6 + - - +
1145D LYS* 2.9 24.9 + - - -
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Residues in contact with LYS1142 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1138D GLU 2.9 15.9 + - - -
1139D VAL* 3.0 5.5 + - - +
1141D LYS* 1.3 75.0 - - - +
1143D ILE* 1.3 63.1 + - - +
1145D LYS* 3.2 10.5 + - - +
1146D LYS 3.7 8.1 + - - -
1165D ILE* 5.4 9.3 - - - -
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Residues in contact with ILE1143 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1139D VAL 2.9 13.5 + - - -
1140D VAL* 3.1 3.6 + - - +
1142D LYS* 1.3 76.4 - - - +
1144D GLU* 1.3 52.9 + - - +
1146D LYS 2.7 24.3 - - - +
1148D PHE 4.9 2.1 + - - +
1165D ILE* 6.1 2.9 - - - +
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Residues in contact with GLU1144 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1140D VAL 3.0 13.0 + - - -
1141D LYS* 3.6 4.9 - - - +
1143D ILE* 1.3 76.6 - - - +
1145D LYS* 1.3 65.6 - - - +
1146D LYS 3.6 5.2 - - - +
1147D ASN* 4.5 2.8 + - - -
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Residues in contact with LYS1145 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1141D LYS 2.9 13.3 + - - -
1142D LYS* 3.2 7.4 + - - +
1144D GLU* 1.3 78.7 - - - +
1146D LYS* 1.3 58.3 + - - +
1147D ASN 3.7 1.7 + - - -
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Residues in contact with LYS1146 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142D LYS 3.7 8.7 + - - -
1143D ILE* 2.7 26.6 - - - +
1144D GLU 3.6 3.0 - - - +
1145D LYS* 1.3 73.1 - - - +
1147D ASN* 1.3 61.4 + - - +
1148D PHE 3.4 4.0 + - - -
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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
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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