Contacts of the helix formed by residues 1136 - 1142 (chain B) in PDB entry 4DAJ
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 SER1136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1114B PHE* 3.3 33.2 - - - -
1132B ASN 4.0 3.7 + - - -
1133B LEU* 2.8 21.5 + - - +
1134B ALA 3.3 0.6 - - - -
1135B LYS* 1.3 80.2 - - - +
1137B ARG* 1.3 62.6 + - - +
1138B TRP* 3.6 12.0 + - - -
1139B TYR* 3.3 17.3 + - - +
1140B ASN* 3.1 26.5 + - - -
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Residues in contact with ARG1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114B PHE* 5.1 0.8 - - + -
1136B SER* 1.3 73.5 - - - +
1138B TRP* 1.3 61.4 + - - +
1139B TYR 3.2 0.4 - - - -
1140B ASN* 3.2 10.4 + - - +
1141B GLN* 2.9 40.6 + - + +
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Residues in contact with TRP1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101B ASN* 5.8 0.9 - - - -
1102B MET* 4.1 30.7 - - + +
1105B GLN* 3.1 26.2 + - - +
1106B MET* 3.5 48.9 - - + +
1114B PHE* 4.5 6.9 - + + -
1133B LEU* 4.8 10.1 - - + -
1136B SER* 3.8 13.2 - - - +
1137B ARG* 1.3 80.3 - - - +
1139B TYR* 1.3 69.4 + - + +
1141B GLN* 4.2 6.5 - - + +
1142B THR* 2.9 41.1 + - - +
1145B ARG* 4.5 3.6 - - + -
1146B ALA* 3.3 42.4 - - + -
1149B VAL* 4.1 23.6 - - + -
1150B ILE* 4.7 12.1 - - + -
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Residues in contact with TYR1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133B LEU 3.9 1.3 - - - +
1134B ALA* 3.1 51.1 - - + +
1136B SER* 3.3 13.8 + - - +
1137B ARG 3.2 0.8 - - - -
1138B TRP* 1.3 81.8 - + + +
1140B ASN* 1.3 72.9 + - - +
1142B THR 3.1 20.1 - - - +
1143B PRO* 3.1 14.5 - - + +
1146B ALA* 3.4 27.8 - - + -
1147B LYS* 3.6 31.1 - - + +
1150B ILE* 4.0 13.2 - - + -
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Residues in contact with ASN1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B LYS 4.8 4.0 + - - -
1136B SER 3.1 22.2 + - - -
1137B ARG* 3.2 10.9 + - - +
1139B TYR* 1.3 90.8 - - - +
1141B GLN* 1.3 64.8 - - + +
1142B THR 3.3 0.2 + - - -
1143B PRO* 3.7 10.2 - - - +
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Residues in contact with GLN1141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021B THR* 5.2 8.7 + - - +
1022B GLU* 5.2 12.1 - - - +
1137B ARG* 2.9 26.4 + - + +
1138B TRP* 4.2 6.9 - - + +
1140B ASN* 1.3 77.7 - - + +
1142B THR* 1.3 70.6 + - + +
1143B PRO* 3.6 5.2 - - - +
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Residues in contact with THR1142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021B THR* 4.3 22.7 - - + +
1105B GLN* 3.6 25.0 + - - +
1138B TRP* 2.9 31.7 + - - -
1139B TYR 3.1 3.3 - - - +
1141B GLN* 1.3 88.8 - - + +
1143B PRO* 1.3 60.4 - - - +
1144B ASN 3.5 2.0 - - - -
1145B ARG* 4.6 11.6 - - + +
1146B ALA* 3.0 27.4 + - - +
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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