Contacts of the helix formed by residues 1086 - 1103 (chain A) in PDB entry 4N4F
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 LYS1086 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A ILE* 3.7 4.6 + - - +
1085A PHE* 1.3 74.7 - - - +
1087A PRO* 1.3 73.8 - - + +
1088A GLU* 3.1 13.6 + - + +
1089A GLU* 3.1 47.9 + - + +
1090A LEU* 3.3 7.5 + - - +
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Residues in contact with PRO1087 (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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1085A PHE 4.2 3.1 - - - +
1086A LYS* 1.3 88.9 - - + +
1088A GLU* 1.3 57.7 + - - +
1090A LEU* 3.4 9.4 + - + +
1091A ARG* 2.9 29.2 + - - +
1142A LEU 4.4 5.3 - - - +
1145A GLY* 3.8 34.5 - - - +
1147A TYR 5.6 2.9 - - - +
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Residues in contact with GLU1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086A LYS* 3.2 13.8 - - + +
1087A PRO* 1.3 76.0 - - - +
1089A GLU* 1.3 60.6 + - - +
1091A ARG* 3.5 25.5 - - - -
1092A GLN* 3.0 45.3 + - + +
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Residues in contact with GLU1089 (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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1083A LYS* 2.9 33.7 + - - -
1084A ILE 4.1 1.0 - - - +
1085A PHE* 3.6 18.1 - - + -
1086A LYS* 3.1 47.6 + - + +
1088A GLU* 1.3 78.3 - - - +
1090A LEU* 1.3 57.6 + - + +
1092A GLN* 4.0 3.5 - - - +
1093A ALA* 3.1 30.0 + - - +
1196A LEU* 4.2 14.3 - - + +
1288A ARG* 5.6 0.3 + - - -
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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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1085A PHE* 3.8 47.6 - - + +
1086A LYS 3.3 7.8 + - - +
1087A PRO* 3.7 9.2 - - + +
1088A GLU 3.3 0.2 - - - -
1089A GLU* 1.3 77.8 - - - +
1091A ARG* 1.3 61.6 + - - +
1093A ALA* 4.9 0.7 - - - -
1094A LEU* 2.9 45.4 + - + +
1142A LEU* 4.4 7.6 - - + -
1147A TYR* 3.3 37.9 - - + +
1148A GLN 3.9 7.6 - - - +
1149A GLU* 4.1 3.8 - - - +
1150A PRO* 4.1 24.2 - - + -
1196A LEU* 4.3 8.5 - - + -
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Residues in contact with ARG1091 (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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1087A PRO 2.9 17.6 + - - +
1088A GLU* 3.5 26.2 - - - +
1090A LEU* 1.3 75.9 - - - +
1092A GLN* 1.3 58.9 + - - +
1095A MET* 2.8 67.8 + - + +
1099A GLU* 5.4 0.6 + - - -
1139A LYS* 3.9 9.7 - - - +
1142A LEU* 4.1 23.9 - - - +
1143A ASP* 2.4 39.4 + - - +
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Residues in contact with GLN1092 (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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1088A GLU* 3.0 32.3 + - - +
1089A GLU* 4.2 3.3 - - - +
1091A ARG* 1.3 80.2 - - - +
1093A ALA* 1.3 62.6 + - - +
1095A MET* 5.3 0.2 - - - -
1096A PRO* 3.5 16.3 - - - +
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Residues in contact with ALA1093 (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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1089A GLU 3.1 19.4 + - - +
1090A LEU 4.1 0.9 - - - +
1092A GLN* 1.3 80.5 - - - +
1094A LEU* 1.3 61.1 + - - +
1096A PRO* 3.6 8.1 - - - +
1097A THR* 4.6 0.5 - - - +
1192A VAL* 3.0 28.6 - - + +
1195A SER* 4.3 6.5 - - - +
1196A LEU* 3.7 35.4 - - + -
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Residues in contact with LEU1094 (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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1090A LEU* 2.9 29.2 + - + +
1093A ALA* 1.3 74.3 - - - +
1095A MET* 1.3 67.1 + - - +
1096A PRO* 3.2 2.9 - - - -
1097A THR* 2.7 25.4 + - - -
1098A LEU 3.3 2.6 + - - -
1142A LEU* 4.1 15.5 - - + -
1147A TYR* 5.6 0.7 - - + -
1150A PRO* 4.0 20.4 - - + -
1153A TYR* 3.7 53.3 + - + -
1189A ILE* 4.5 8.5 - - + -
1192A VAL* 3.9 19.5 - - + -
1193A MET* 4.6 3.4 - - - -
1196A LEU* 4.1 16.6 - - + -
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Residues in contact with MET1095 (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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1091A ARG* 2.8 42.8 + - + +
1092A GLN* 5.3 0.2 - - - -
1094A LEU* 1.3 78.0 - - - +
1096A PRO* 1.3 68.7 - - + +
1098A LEU* 2.8 17.4 + - - +
1099A GLU* 2.8 46.4 + - - +
1102A TYR* 6.2 0.7 - - - -
1139A LYS* 3.8 26.0 - - + -
1142A LEU* 3.7 32.9 - - + +
1143A ASP* 3.7 23.1 - - - +
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Residues in contact with PRO1096 (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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1092A GLN* 3.5 21.8 - - - +
1093A ALA 3.6 6.3 - - - +
1094A LEU 3.4 3.4 - - - -
1095A MET* 1.3 94.9 - - + +
1097A THR* 1.3 57.2 + - + +
1099A GLU* 3.5 18.3 - - - +
1100A ALA* 2.9 28.1 + - - +
1103A ARG* 3.8 7.5 + - - +
1188A GLU* 5.0 3.3 - - - +
1192A VAL* 5.8 2.7 - - + -
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Residues in contact with THR1097 (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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1094A LEU 2.7 13.0 + - - +
1096A PRO* 1.3 75.7 - - + +
1098A LEU* 1.3 60.2 + - - +
1100A ALA* 3.3 15.8 + - - +
1101A LEU* 3.5 17.3 + - - +
1153A TYR* 2.6 36.2 + - - -
1185A PHE* 3.9 12.9 - - - -
1188A GLU* 4.0 25.0 - - + +
1189A ILE* 4.2 9.9 - - + -
1192A VAL* 3.8 37.0 - - + -
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Residues in contact with LEU1098 (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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1094A LEU 3.3 1.3 + - - +
1095A MET* 2.8 25.1 + - - +
1097A THR* 1.3 76.9 + - - +
1099A GLU* 1.3 62.7 + - - +
1100A ALA 3.2 0.2 - - - -
1101A LEU* 3.1 13.8 + - + +
1102A TYR* 2.9 40.7 + - + -
1135A LEU* 3.4 31.2 - - + +
1138A ILE* 3.9 25.1 - - + -
1139A LYS* 3.7 40.8 - - + +
1142A LEU* 4.3 4.0 - - + -
1153A TYR* 3.5 17.3 - - + +
1157A VAL* 4.9 1.1 - - + -
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Residues in contact with GLU1099 (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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1091A ARG* 5.4 0.9 + - - -
1095A MET* 2.8 37.7 + - + +
1096A PRO* 3.5 23.6 - - - +
1098A LEU* 1.3 73.6 - - - +
1100A ALA* 1.3 65.5 + - - +
1102A TYR* 3.1 12.5 + - + +
1103A ARG* 2.9 38.6 + - + +
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Residues in contact with ALA1100 (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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1096A PRO 2.9 13.7 + - - +
1097A THR 3.5 11.2 - - - +
1098A LEU 3.2 0.6 - - - -
1099A GLU* 1.3 76.6 - - - +
1101A LEU* 1.3 59.4 + - - +
1103A ARG* 3.5 29.3 - - - +
1104A GLN* 2.9 30.2 + - - +
1184A VAL* 3.9 8.7 - - + +
1188A GLU* 3.9 29.6 - - + +
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Residues in contact with LEU1101 (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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1097A THR 3.6 12.1 - - - +
1098A LEU* 3.1 15.7 + - + +
1099A GLU 3.1 0.6 - - - -
1100A ALA* 1.3 74.8 - - - +
1102A TYR* 1.3 65.4 + - - +
1104A GLN* 2.9 19.6 + - - +
1108A SER* 3.2 14.8 - - - -
1135A LEU* 3.8 26.7 - - + -
1157A VAL* 4.4 5.8 - - + -
1160A MET* 4.4 1.6 - - + -
1161A PHE* 4.1 19.7 - - + -
1181A LEU* 3.4 39.4 - - + +
1184A VAL* 3.9 16.8 - - + -
1185A PHE* 4.0 22.9 - - + +
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Residues in contact with TYR1102 (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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1095A MET* 6.2 0.7 - - - -
1098A LEU* 2.9 44.9 + - + -
1099A GLU* 3.6 12.8 - - + +
1101A LEU* 1.3 75.4 - - - +
1103A ARG* 1.3 60.1 + - - +
1108A SER* 3.0 9.0 + - - -
1112A ARG* 2.8 68.0 + - + +
1135A LEU* 3.3 42.2 + - + +
1136A SER* 3.4 11.4 + - - -
1139A LYS* 4.2 19.9 - - + +
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Residues in contact with ARG1103 (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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1096A PRO* 3.8 11.9 + - - +
1099A GLU* 2.9 23.2 + - + +
1100A ALA* 3.5 46.7 + - - +
1101A LEU 3.1 0.4 - - - -
1102A TYR* 1.3 76.0 - - - +
1104A GLN* 1.3 73.1 + - - +
1105A ASP* 3.2 8.7 + - - +
1112A ARG* 5.0 0.6 + - - -
1188A GLU* 5.1 6.1 + - - -
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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