Contacts of the helix formed by residues 1125 - 1135 (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 ARG1125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482B LEU 5.7 1.6 - - - +
484B LYS* 3.6 35.6 - - - +
1005B GLU* 5.3 2.0 - - - +
1009B ILE* 5.9 2.7 - - + -
1120C MET* 3.1 39.2 + - + +
1123C GLN* 2.8 42.7 + - + +
1124C LYS* 1.3 77.0 - - - +
1126C TRP* 1.3 64.4 + - - +
1127C ASP 3.9 0.4 - - - -
1128C GLU* 2.5 47.1 + - + +
1129C ALA* 3.4 16.7 + - - +
2002C PO4 3.7 19.6 + - - -
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Residues in contact with TRP1126 (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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1008B ARG* 3.0 53.5 - - + +
1009B ILE* 5.0 10.6 + - - +
1091C LEU* 3.8 16.8 - - + -
1092C ASP* 4.8 0.2 - - - -
1095C ARG* 3.2 58.1 - - - +
1121C LEU* 3.5 34.5 - - + -
1124C LYS* 3.5 47.4 + - + +
1125C ARG* 1.3 72.1 - - - +
1127C ASP* 1.3 68.5 + - - +
1128C GLU 3.2 1.3 - - - -
1129C ALA* 3.0 7.0 + - - +
1130C ALA* 2.9 21.0 + - - +
1153C PHE 3.6 6.5 - - - -
1154C ARG* 3.8 13.5 - - - +
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Residues in contact with ASP1127 (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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173B LEU* 3.2 26.4 - - + +
177B ALA* 4.1 15.0 - - + -
1004B PHE* 4.9 3.3 - - - -
1008B ARG* 3.2 26.4 + - - +
1013B LEU* 3.1 24.3 - - - +
1126C TRP* 1.3 74.1 + - - +
1128C GLU* 1.3 59.3 + - + +
1130C ALA* 3.1 5.5 + - - +
1131C VAL* 2.9 33.5 + - + +
1154C ARG* 3.5 27.5 + - - +
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Residues in contact with GLU1128 (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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176B ARG* 4.0 26.9 + - - +
177B ALA* 3.9 27.3 - - + +
484B LYS* 5.2 1.9 + - - -
1005B GLU* 5.2 1.6 - - - +
1120C MET* 4.2 13.1 - - - +
1125C ARG* 2.5 55.4 + - + +
1126C TRP 3.2 0.6 - - - -
1127C ASP* 1.3 75.9 - - + +
1129C ALA* 1.3 57.4 + - - +
1131C VAL* 3.0 13.2 + - - +
1132C ASN* 2.9 30.9 + - - +
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Residues in contact with ALA1129 (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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1117C SER* 3.7 23.0 + - - +
1120C MET* 3.7 17.6 - - + +
1121C LEU* 4.2 17.0 - - + -
1125C ARG 3.4 15.2 + - - +
1126C TRP* 3.0 9.5 + - - +
1128C GLU* 1.3 77.7 - - - +
1130C ALA* 1.3 57.5 + - - +
1132C ASN* 3.3 4.3 + - - +
1133C LEU* 2.9 34.5 + - + +
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Residues in contact with ALA1130 (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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1126C TRP 2.9 5.7 + - - -
1127C ASP 3.3 9.4 - - - +
1129C ALA* 1.3 72.7 - - - +
1131C VAL* 1.3 66.0 + - - +
1133C LEU* 3.1 9.2 + - + +
1134C ALA* 3.0 25.6 + - - +
1150C ILE* 3.3 33.3 - - + +
1153C PHE* 5.8 1.6 - - + -
1154C ARG* 3.6 31.0 - - + +
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Residues in contact with VAL1131 (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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173B LEU 5.5 0.2 - - - +
177B ALA* 3.7 28.9 - - + +
178B LYS* 3.7 47.1 - - + +
180B THR* 5.6 4.9 - - + -
183B ARG* 6.0 0.7 - - - +
1060B LYS* 6.1 0.9 - - - +
1127C ASP* 2.9 21.2 + - + +
1128C GLU 3.1 7.2 - - - +
1130C ALA* 1.3 78.5 - - + +
1132C ASN* 1.3 65.7 - - - +
1133C LEU 3.2 0.7 + - - -
1134C ALA* 3.4 11.8 + - - +
1135C LYS* 3.6 10.0 + - - +
1154C ARG* 5.6 4.7 - - - +
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Residues in contact with ASN1132 (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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177B ALA 5.5 2.0 + - - -
180B THR* 5.8 5.9 - - - +
1114C PHE* 5.5 2.4 - - - -
1116C ASN* 3.3 19.2 - - + +
1117C SER* 3.3 19.3 + - - +
1120C MET* 3.1 36.7 - - + +
1128C GLU* 2.9 13.3 + - - +
1129C ALA 3.7 1.6 - - - +
1131C VAL* 1.3 79.8 - - - +
1133C LEU* 1.3 62.7 + - - +
1135C LYS* 3.5 16.9 + - - +
1136C SER* 4.2 3.8 + - - -
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Residues in contact with LEU1133 (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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1102C MET* 4.9 20.0 - - + -
1114C PHE* 5.0 11.0 - - + -
1117C SER* 3.5 22.9 - - - +
1118C LEU* 6.5 0.2 - - + -
1121C LEU* 6.0 4.7 - - + -
1129C ALA* 2.9 25.6 + - + +
1130C ALA* 3.2 14.1 - - - +
1131C VAL 3.1 0.2 - - - -
1132C ASN* 1.3 74.5 - - - +
1134C ALA* 1.3 55.2 + - - +
1135C LYS 2.7 15.8 + - - -
1136C SER* 2.9 26.1 + - - -
1138C TRP* 4.8 8.8 - - + -
1139C TYR* 4.0 1.8 - - - +
1149C VAL* 5.9 0.4 - - + -
1150C ILE* 3.6 30.3 - - + -
1153C PHE* 4.5 27.1 - - + -
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Residues in contact with ALA1134 (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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178B LYS* 6.2 1.8 - - - +
1130C ALA 3.0 14.9 + - - +
1131C VAL* 3.4 7.3 + - - +
1133C LEU* 1.3 74.2 - - - +
1135C LYS* 1.3 58.8 + - - +
1136C SER 3.3 2.2 + - - +
1139C TYR* 3.6 50.6 - - + +
1150C ILE* 3.9 2.6 - - + +
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Residues in contact with LYS1135 (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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1131C VAL 3.6 8.1 + - - +
1132C ASN* 3.5 16.3 + - - +
1133C LEU 2.7 1.2 + - - -
1134C ALA* 1.3 76.8 - - - +
1136C SER* 1.3 65.5 + - - +
1140C ASN* 5.7 0.2 - - - +
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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