Contacts of the helix formed by residues 1136 - 1142 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1114C PHE* 3.2 33.7 - - - -
1132C ASN 4.2 2.3 + - - -
1133C LEU* 2.9 15.9 + - - +
1134C ALA 3.3 3.1 - - - +
1135C LYS* 1.3 84.8 - - - +
1137C ARG* 1.3 62.8 + - - +
1138C TRP* 3.4 11.8 + - - +
1139C TYR 3.3 16.3 + - - -
1140C ASN* 3.6 19.4 + - - +
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Residues in contact with ARG1137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106C MET* 6.2 1.3 - - - -
1114C PHE* 6.0 2.2 - - + -
1136C SER* 1.3 74.3 - - - +
1138C TRP* 1.3 65.9 + - + +
1140C ASN* 3.2 10.5 + - + +
1141C GLN* 2.9 39.6 + - + +
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Residues in contact with TRP1138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101C ASN* 5.7 0.2 - - - -
1102C MET* 4.6 20.2 - - + +
1105C GLN* 4.9 11.8 - - + +
1106C MET* 3.5 51.2 - - + +
1114C PHE* 4.3 6.3 - + + -
1133C LEU* 4.8 11.7 - - + -
1136C SER* 3.6 13.2 - - - +
1137C ARG* 1.3 81.9 - - + +
1139C TYR* 1.3 82.9 + - + +
1141C GLN* 3.2 7.3 + - + +
1142C THR* 3.1 35.0 + - - -
1145C ARG* 4.3 12.8 - - + +
1146C ALA* 3.2 43.1 - - + -
1149C VAL* 4.1 24.2 - - + -
1150C ILE* 4.4 17.3 - - + -
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Residues in contact with TYR1139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134C ALA* 3.6 49.1 - - + +
1136C SER* 3.3 8.8 + - - +
1138C TRP* 1.3 86.1 - - + +
1140C ASN* 1.3 69.2 + - - +
1142C THR 3.4 15.8 - - - -
1143C PRO* 3.4 12.5 - - + +
1146C ALA* 3.3 32.3 - - + -
1147C LYS* 3.4 34.6 - - + +
1150C ILE* 3.7 18.4 - - + -
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Residues in contact with ASN1140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136C SER 3.6 13.5 + - - +
1137C ARG* 3.2 14.0 + - - +
1138C TRP 3.1 0.2 - - - -
1139C TYR* 1.3 86.7 - - - +
1141C GLN* 1.3 67.0 + - + +
1143C PRO* 4.1 6.6 - - - +
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Residues in contact with GLN1141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021C THR* 5.4 8.0 + - - -
1022C GLU* 5.3 17.3 - - + +
1137C ARG* 2.9 28.6 + - + +
1138C TRP* 3.2 6.5 + - + +
1140C ASN* 1.3 81.9 - - - +
1142C THR* 1.3 69.2 + - + +
1143C PRO* 3.4 7.3 - - - +
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Residues in contact with THR1142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021C THR* 4.0 30.7 - - + +
1138C TRP* 3.1 25.5 + - - +
1139C TYR 3.4 3.5 - - - +
1141C GLN* 1.3 86.9 - - + +
1143C PRO* 1.3 62.7 - - - +
1144C ASN* 3.4 4.3 - - - +
1145C ARG* 4.3 19.8 - - + +
1146C ALA* 3.1 24.6 + - - +
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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