Contacts of the helix formed by residues 1085 - 1096 (chain A) in PDB entry 1N35
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 ASN1085 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A GLY 3.1 17.6 + - - -
833A LEU 2.7 25.6 + - - -
834A GLN* 3.6 12.3 - - - +
835A TRP* 3.1 35.0 + - - -
1080A GLY 3.1 22.1 + - - +
1081A ILE* 4.2 3.6 - - - +
1082A ASP* 2.8 10.8 + - - +
1084A LEU* 1.3 78.5 - - - +
1086A SER* 1.3 63.8 + - - +
1087A ASP 3.6 0.9 - - - -
1088A PRO* 3.1 15.4 - - - +
1089A PHE* 3.0 18.2 + - - +
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Residues in contact with SER1086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASP* 2.7 37.7 + - - -
171A VAL* 3.8 19.4 - - - +
172A LEU* 4.1 11.9 - - - -
835A TRP* 3.0 13.4 + - - +
1082A ASP 4.1 0.2 + - - -
1083A PRO 4.3 4.8 + - - -
1084A LEU 3.6 3.2 + - - -
1085A ASN* 1.3 72.6 - - - +
1087A ASP* 1.3 62.2 + - - -
1089A PHE* 4.4 4.3 - - - -
1090A LEU* 2.8 39.9 + - - +
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Residues in contact with ASP1087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 5.2 0.2 - - - +
835A TRP* 3.4 27.9 - - + +
889A SER* 2.8 33.4 + - - -
890A TRP* 4.2 5.7 + - - -
891A TYR* 4.0 7.1 - - - -
1086A SER* 1.3 80.3 + - - +
1088A PRO* 1.3 77.1 - - + +
1090A LEU* 3.7 1.5 - - - +
1091A LYS* 2.9 44.1 + - - +
1234A THR* 3.5 4.2 - - + -
1235A GLY* 3.1 27.4 + - - +
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Residues in contact with PRO1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A TRP* 3.4 13.7 - - + -
890A TRP* 3.5 31.2 - - + +
891A TYR* 3.8 22.1 + - + +
1081A ILE* 3.7 29.1 - - + +
1085A ASN* 3.1 26.9 - - - +
1087A ASP* 1.3 91.4 - - + +
1089A PHE* 1.3 55.0 + - - +
1091A LYS* 3.4 1.6 + - - +
1092A MET* 2.9 30.3 + - - +
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Residues in contact with PHE1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A PHE* 3.8 23.1 - + - -
1073A LEU* 3.5 37.0 - - + -
1075A LEU 5.1 3.4 - - - -
1081A ILE* 3.7 14.5 - - + +
1082A ASP* 3.2 36.8 - - - +
1083A PRO* 3.8 24.9 - - + -
1085A ASN 3.0 11.0 + - - +
1086A SER* 3.7 3.8 - - - +
1088A PRO* 1.3 75.1 - - - +
1090A LEU* 1.3 76.0 + - + +
1092A MET* 3.4 4.1 + - + +
1093A VAL* 3.0 59.3 + - + +
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Residues in contact with LEU1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.5 32.8 - - + -
1073A LEU* 5.8 4.9 - - + -
1086A SER* 2.8 29.7 + - - +
1087A ASP 3.8 0.2 - - - +
1089A PHE* 1.3 87.8 - - + +
1091A LYS* 1.3 60.2 + - - +
1093A VAL* 4.1 5.5 - - + +
1094A SER* 2.8 34.5 + - - -
1235A GLY* 3.7 35.2 - - - +
1236A VAL* 3.9 20.8 - - + +
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Residues in contact with LYS1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A SER* 3.7 3.6 + - - -
891A TYR* 3.7 26.9 - - + -
1087A ASP* 2.9 34.7 + - - +
1088A PRO 3.7 1.1 - - - +
1090A LEU* 1.3 75.0 - - - +
1092A MET* 1.3 64.7 + - - +
1094A SER* 4.0 2.2 - - - -
1095A VAL* 2.9 36.7 + - + +
1187A LEU* 4.4 6.5 - - + -
1230A VAL 3.8 14.4 - - - -
1231A MET* 3.2 41.5 + - + +
1233A ALA 2.8 27.1 + - - -
1235A GLY 3.3 14.3 + - - +
1236A VAL 4.5 0.7 - - - -
1237A ALA* 4.4 10.1 - - - +
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Residues in contact with MET1092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A TYR* 5.7 3.6 - - - +
1071A VAL* 4.3 1.2 - - + +
1077A LEU* 4.5 28.3 - - + -
1078A CYS* 5.4 8.3 - - + -
1081A ILE* 4.3 18.6 - - + -
1088A PRO 2.9 18.4 + - - +
1089A PHE* 3.5 6.7 - - + +
1090A LEU 3.4 0.2 - - - -
1091A LYS* 1.3 77.4 - - - +
1093A VAL* 1.3 61.3 + - + +
1096A GLY* 2.8 30.7 + - - -
1097A PRO* 3.8 33.1 - - + +
1186A SER* 4.4 15.5 - - - +
1187A LEU* 3.8 24.8 - - + +
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Residues in contact with VAL1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069A PRO* 4.0 7.2 - - + -
1070A SER* 2.9 29.8 + - - -
1071A VAL* 3.5 33.6 + - + +
1072A ASP 5.2 0.7 - - - +
1073A LEU* 3.6 29.6 - - + -
1077A LEU* 6.4 0.7 - - + -
1089A PHE* 3.0 50.5 + - + +
1090A LEU* 4.1 5.6 - - + +
1092A MET* 1.3 81.7 - - + +
1094A SER* 1.3 60.2 + - - +
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Residues in contact with SER1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067A ARG* 3.4 28.7 + - - -
1068A GLU 3.9 8.7 - - - +
1069A PRO* 4.7 1.1 - - - -
1070A SER* 2.7 19.6 + - - -
1090A LEU 2.8 22.7 + - - -
1091A LYS* 3.8 1.9 + - - -
1093A VAL* 1.3 78.2 - - - +
1095A VAL* 1.3 60.9 + - - +
1236A VAL* 4.4 8.5 - - - -
1237A ALA* 2.8 38.0 + - - +
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Residues in contact with VAL1095 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067A ARG* 4.0 18.1 + - - +
1070A SER* 3.8 5.7 + - - -
1091A LYS* 2.9 24.8 + - + +
1094A SER* 1.3 77.0 - - - +
1096A GLY* 1.3 58.7 + - - +
1187A LEU* 3.9 25.4 - - + -
1188A ASP* 3.6 32.9 - - - +
1189A PHE* 4.7 1.6 - - - +
1191A SER* 5.2 0.5 - - - -
1192A MET* 5.1 7.9 - - + -
1231A MET* 4.0 24.9 - - + -
1237A ALA* 3.3 26.2 - - + -
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Residues in contact with GLY1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070A SER* 3.9 15.9 - - - -
1071A VAL* 4.9 0.4 - - - -
1092A MET 2.8 17.6 + - - -
1094A SER 3.4 1.8 - - - -
1095A VAL* 1.3 78.0 - - - +
1097A PRO* 1.3 68.9 - - - +
1187A LEU* 3.4 9.2 - - - +
1188A ASP* 2.7 30.1 + - - -
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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