Contacts of the helix formed by residues 1104 - 1116 (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 ASN1104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1069A TYR* 3.8 3.0 - - - -
1070A SER 2.7 15.7 + - - +
1071A ASP* 3.6 30.3 + - - +
1102A THR* 3.6 9.0 + - - -
1103A PRO* 1.3 67.4 - - - +
1105A THR* 1.3 64.5 + - - +
1106A GLY 3.3 2.9 + - - -
1107A ALA* 3.5 9.1 + - + +
1108A ALA* 3.1 22.2 + - - +
1142A GLY* 3.2 27.9 - - - +
1143A ASP* 3.5 20.7 - - - +
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Residues in contact with THR1105 (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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1030A LEU* 5.5 0.9 - - + -
1069A TYR* 2.7 36.9 + - + +
1103A PRO* 3.0 12.2 + - - +
1104A ASN* 1.3 71.7 - - - +
1106A GLY* 1.3 58.3 + - - +
1108A ALA* 3.3 1.4 + - - +
1109A LEU* 2.9 41.4 + - + +
1135A VAL* 4.5 9.2 - - + -
1137A THR* 4.3 5.1 + - + +
1139A GLU 5.5 0.2 + - - -
1141A SER* 3.1 20.3 + - - -
1145A VAL* 3.9 1.6 - - + -
1172A MET* 5.3 4.5 - - + -
1175A ILE* 3.7 29.4 - - + -
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Residues in contact with GLY1106 (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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1105A THR* 1.3 72.3 - - - +
1107A ALA* 1.3 60.3 + - - -
1109A LEU* 3.2 3.5 + - - -
1110A GLU* 3.1 20.1 + - - +
1143A ASP* 2.8 20.5 + - - -
1144A ASP 3.6 17.3 - - - -
1145A VAL* 3.8 7.3 - - - +
1148A PRO* 3.5 27.0 - - - +
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Residues in contact with ALA1107 (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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1073A THR* 5.2 1.8 - - + -
1104A ASN* 3.9 11.7 - - + +
1105A THR 3.4 0.2 - - - -
1106A GLY* 1.3 74.4 - - - +
1108A ALA* 1.3 57.3 + - - +
1110A GLU* 3.4 6.5 + - - +
1111A PHE* 2.9 29.7 + - - +
1143A ASP* 2.9 18.3 + - - +
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Residues in contact with ALA1108 (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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1030A LEU* 4.0 9.6 - - + +
1069A TYR* 3.4 44.2 - - + -
1073A THR* 3.9 14.3 - - + +
1104A ASN 3.1 13.9 + - - +
1105A THR 3.6 4.0 - - - +
1106A GLY 3.2 0.2 - - - -
1107A ALA* 1.3 77.6 - - - +
1109A LEU* 1.3 62.1 + - - +
1111A PHE* 3.3 3.1 + - - +
1112A VAL* 3.0 27.5 + - - +
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Residues in contact with LEU1109 (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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1030A LEU* 3.9 20.0 - - + -
1105A THR* 2.9 25.2 + - + +
1106A GLY* 3.2 11.4 + - - +
1108A ALA* 1.3 75.6 - - - +
1110A GLU* 1.3 62.5 + - - +
1112A VAL* 3.2 5.8 + - - +
1113A LEU 3.0 17.8 + - - -
1133A LEU* 3.9 10.1 - - + -
1135A VAL* 4.0 14.8 - - + -
1145A VAL* 4.7 2.9 - - + -
1148A PRO* 4.4 10.5 - - + -
1149A SER* 4.8 6.1 - - - +
1152A LEU* 3.4 37.0 - - + +
1175A ILE* 3.8 38.8 - - + -
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Residues in contact with GLU1110 (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 3.1 7.5 + - - +
1107A ALA* 3.9 6.0 - - - +
1109A LEU* 1.3 72.3 - - - +
1111A PHE* 1.3 65.4 + - - +
1113A LEU* 3.2 2.2 + - - +
1114A ARG* 2.9 43.9 + - + +
1147A GLY 4.5 0.5 - - - -
1148A PRO* 3.7 35.3 - - + +
1151A VAL* 3.6 30.8 - - + +
1152A LEU* 4.1 10.3 - - + -
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Residues in contact with PHE1111 (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 VAL* 4.2 9.6 - - + -
1073A THR* 3.6 40.8 - - + -
1075A PRO* 3.7 31.4 - - + -
1107A ALA 2.9 17.6 + - - +
1108A ALA 3.5 5.4 - - - +
1110A GLU* 1.3 76.1 - - - +
1112A VAL* 1.3 66.0 + - - +
1114A ARG* 5.0 0.2 - - - -
1115A ASN* 2.9 62.7 + - + +
1116A ILE* 3.9 16.8 - - + -
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Residues in contact with VAL1112 (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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1028A VAL* 4.3 7.4 - - + -
1030A LEU* 3.9 30.1 - - + -
1067A VAL* 4.5 16.6 - - + -
1108A ALA 3.0 17.9 + - - +
1109A LEU* 3.2 8.5 + - - +
1111A PHE* 1.3 80.0 - - + +
1113A LEU* 1.3 65.1 + - - +
1116A ILE* 2.9 33.8 + - + -
1117A LEU* 2.9 26.5 + - + -
1133A LEU* 4.0 27.8 - - + -
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Residues in contact with LEU1113 (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 3.0 6.7 + - - -
1110A GLU* 3.2 6.9 + - - +
1112A VAL* 1.3 78.4 - - - +
1114A ARG* 1.3 79.7 + - + +
1115A ASN 3.6 0.2 + - - -
1117A LEU* 3.8 40.8 + - + +
1118A THR* 4.2 1.2 - - - +
1125A ILE* 5.2 2.9 - - + -
1151A VAL* 3.5 43.1 - - + +
1152A LEU* 3.8 24.4 - - + +
1155A GLY* 4.0 29.8 - - - +
1157A ALA* 4.8 0.9 - - + -
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Residues in contact with ARG1114 (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* 2.9 30.3 + - + +
1113A LEU* 1.3 91.8 - - + +
1115A ASN* 1.3 73.8 + - - +
1118A THR* 3.3 13.2 - - - +
1151A VAL* 3.4 31.9 - - - +
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Residues in contact with ASN1115 (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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1078A TYR* 5.2 0.2 - - - -
1111A PHE* 2.9 58.3 + - + +
1114A ARG* 1.3 92.3 - - - +
1116A ILE* 1.3 63.5 + - + +
1118A THR* 3.2 18.7 + - - -
1121A THR* 3.4 14.9 + - - +
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Residues in contact with ILE1116 (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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1028A VAL* 4.2 32.1 - - + -
1065A ALA* 4.3 13.7 - - + -
1067A VAL* 4.0 17.3 - - + -
1075A PRO* 4.2 3.1 - - + -
1077A PHE 5.7 0.4 - - - +
1078A TYR* 3.6 35.2 - - + -
1079A LEU* 3.8 15.5 + - + +
1111A PHE* 3.9 25.4 - - + -
1112A VAL* 2.9 24.7 + - + +
1115A ASN* 1.3 81.5 - - + +
1117A LEU* 1.3 59.9 + - - +
1118A THR 3.1 7.3 + - - -
1121A THR* 3.1 16.0 + - - -
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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