Contacts of the helix formed by residues 1145 - 1155 (chain A) in PDB entry 4IGI
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 VAL1145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105A THR* 3.9 8.3 - - + -
1106A GLY* 3.8 17.0 - - - +
1109A LEU* 4.7 1.9 - - + +
1141A SER* 3.7 32.1 - - - +
1143A ASP 3.5 1.0 + - - +
1144A ASP* 1.3 74.0 + - - +
1146A ARG* 1.3 62.0 + - - +
1147A GLY 3.5 0.9 - - - -
1148A PRO* 3.7 3.9 - - - +
1149A SER* 2.9 30.5 + - - -
1171A GLU* 4.0 33.2 + - + +
1174A THR* 4.4 8.5 - - + -
1175A ILE* 4.1 25.4 - - + -
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Residues in contact with ARG1146 (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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1144A ASP* 3.0 20.3 + - - +
1145A VAL* 1.3 80.0 - - + +
1147A GLY* 1.3 87.9 + - - +
1149A SER* 2.7 25.2 + - - +
1150A VAL* 3.2 14.9 + - - +
1174A THR* 4.3 8.5 - - + -
1219A PRO* 2.9 54.6 - - + +
1220A SER* 3.8 19.1 - - - +
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Residues in contact with GLY1147 (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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1110A GLU* 4.5 0.7 - - - -
1144A ASP* 2.9 14.8 + - - -
1146A ARG* 1.3 95.0 - - - +
1148A PRO* 1.3 69.4 - - - +
1150A VAL* 3.1 7.4 + - - +
1151A VAL* 3.0 27.3 + - - +
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Residues in contact with PRO1148 (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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1106A GLY* 3.5 34.3 - - - +
1109A LEU* 4.4 8.5 - - + -
1110A GLU* 3.7 28.3 - - + +
1144A ASP* 3.4 28.0 - - + +
1145A VAL 3.7 4.9 - - - +
1147A GLY* 1.3 89.8 - - - +
1149A SER* 1.3 61.3 + - - +
1151A VAL* 3.2 1.3 + - + +
1152A LEU* 2.9 30.0 + - - +
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Residues in contact with SER1149 (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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1109A LEU* 4.8 4.9 - - - +
1145A VAL 2.9 16.4 + - - -
1146A ARG* 2.7 18.0 + - - +
1148A PRO* 1.3 75.8 - - - +
1150A VAL* 1.3 65.2 + - - +
1152A LEU* 3.4 5.9 + - - +
1153A LYS* 3.1 33.9 + - - +
1174A THR* 3.3 42.6 + - - +
1175A ILE* 4.0 11.4 - - - +
1219A PRO* 5.6 0.5 - - - +
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Residues in contact with VAL1150 (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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1146A ARG* 3.6 17.9 - - - +
1147A GLY* 3.1 9.3 + - - +
1149A SER* 1.3 82.0 + - - +
1151A VAL* 1.3 61.1 + - + +
1153A LYS* 3.3 3.4 + - + +
1154A GLN* 2.9 60.4 + - - +
1217A LEU* 4.0 26.0 - - + +
1219A PRO* 3.7 28.5 - - + -
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Residues in contact with VAL1151 (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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1110A GLU* 3.6 23.8 - - + +
1113A LEU* 3.5 17.5 - - + +
1114A ARG* 3.4 29.4 - - - +
1147A GLY 3.0 14.0 + - - +
1148A PRO* 3.6 7.0 - - + +
1150A VAL* 1.3 76.7 - - + +
1152A LEU* 1.3 58.8 + - + +
1154A GLN* 3.4 16.0 + - - +
1155A GLY* 3.0 25.8 + - - -
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Residues in contact with LEU1152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1109A LEU* 3.4 48.0 - - + +
1110A GLU* 4.0 7.6 - - + +
1113A LEU* 3.8 24.4 - - + +
1117A LEU* 6.0 0.2 - - + -
1133A LEU* 3.6 31.4 - - + -
1148A PRO 2.9 21.6 + - - +
1149A SER* 3.8 5.4 - - - +
1150A VAL 3.2 0.2 - - - -
1151A VAL* 1.3 78.1 - - - +
1153A LYS* 1.3 64.4 + - - +
1155A GLY 3.1 7.1 + - - -
1156A GLY 3.2 0.2 + - - -
1157A ALA* 3.0 39.7 + - + -
1159A PRO* 4.3 11.0 - - + -
1175A ILE* 5.9 0.2 - - + -
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Residues in contact with LYS1153 (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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1149A SER* 3.1 21.2 + - - +
1150A VAL* 3.8 2.9 - - + +
1152A LEU* 1.3 78.0 - - + +
1154A GLN* 1.3 61.9 + - - +
1155A GLY 3.3 0.3 + - - -
1156A GLY* 3.5 8.5 + - - -
1157A ALA 4.1 9.1 - - - +
1159A PRO* 4.9 4.5 - - + -
1173A GLN 4.7 0.6 + - - -
1174A THR* 2.8 28.3 + - - +
1175A ILE 3.9 6.5 - - - +
1176A SER 3.1 24.1 + - - -
1177A PHE* 3.7 15.4 + - + -
1178A ILE* 5.6 0.2 - - - +
1179A PRO* 6.2 0.6 - - - +
1215A PRO* 4.0 28.5 - - + +
1216A ILE* 2.7 29.7 + - - +
1217A LEU* 3.7 22.5 - - + +
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Residues in contact with GLN1154 (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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1150A VAL* 2.9 42.3 + - + +
1151A VAL* 3.8 16.3 - - - +
1153A LYS* 1.3 76.7 - - - +
1155A GLY* 1.3 59.6 + - - +
1156A GLY 3.4 0.9 + - - -
1217A LEU* 4.4 12.0 - - + +
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Residues in contact with GLY1155 (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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1113A LEU* 4.0 17.8 - - - +
1125A ILE* 3.7 19.4 - - - +
1151A VAL 3.0 16.3 + - - -
1152A LEU 3.1 1.9 + - - -
1154A GLN* 1.3 79.1 - - - +
1156A GLY* 1.3 57.7 + - - +
1157A ALA 3.5 2.7 - - - -
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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