Contacts of the strand formed by residues 1062 - 1069 (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 VAL1062 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A GLU* 5.4 0.9 - - - +
1025A LYS* 3.2 32.8 - - + +
1027A VAL* 3.8 19.1 - - + -
1055A LEU* 3.9 23.1 - - + -
1056A ASP* 2.9 30.6 + - + +
1057A VAL* 3.4 9.5 - - - +
1058A GLY 2.9 26.0 + - - +
1061A ARG* 1.3 85.2 - - + +
1063A ARG* 1.3 69.6 + - - +
1064A VAL* 4.2 4.7 - - + -
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Residues in contact with ARG1063 (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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1025A LYS 3.0 6.3 + - - +
1026A ASP* 3.6 10.3 - - - +
1027A VAL 2.8 27.2 + - - -
1057A VAL* 5.6 0.7 - - - -
1058A GLY 4.2 3.1 - - - +
1059A PRO* 2.8 42.5 + - + +
1060A ASP* 4.8 4.6 + - - -
1062A VAL* 1.3 79.9 - - - +
1064A VAL* 1.3 60.9 + - - +
1079A LEU* 3.4 27.9 + - + +
1080A ASN* 5.1 5.1 - - - +
1082A HIS 5.8 3.6 - - - +
1122A GLY* 2.8 45.0 + - - -
1123A SER 5.0 0.2 - - - -
1124A ARG* 3.5 36.3 - - - +
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Residues in contact with VAL1064 (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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1027A VAL* 3.2 9.9 - - + +
1029A PHE* 3.8 24.9 - - + -
1052A VAL* 4.2 4.0 - - + -
1055A LEU* 4.5 10.5 - - + -
1057A VAL* 4.2 21.2 - - + +
1062A VAL* 4.2 15.3 - - + -
1063A ARG* 1.3 81.1 - - - +
1065A ALA* 1.3 67.7 + - - +
1077A PHE* 3.4 14.1 - - + -
1078A TYR 3.2 16.3 - - - +
1079A LEU* 3.8 4.3 + - - -
1082A HIS* 5.3 2.3 + - - +
1088A VAL* 4.0 35.6 - - + +
1092A ILE* 5.7 0.2 - - + -
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Residues in contact with ALA1065 (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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1027A VAL 2.9 6.8 + - - +
1028A VAL* 3.4 14.3 - - + -
1029A PHE* 2.9 29.2 + - - -
1064A VAL* 1.3 73.5 - - - +
1066A LEU* 1.3 63.9 + - - +
1077A PHE* 3.4 20.9 - - - +
1078A TYR* 3.9 1.6 - - - -
1079A LEU* 3.6 29.4 - - + +
1116A ILE* 4.3 11.4 - - + -
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Residues in contact with LEU1066 (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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1029A PHE* 3.3 18.8 - - + +
1031A ILE* 4.1 13.7 - - + -
1048A VAL* 4.1 28.5 - - + -
1065A ALA* 1.3 75.1 - - - +
1067A VAL* 1.3 68.3 + - - +
1068A GLN* 4.3 5.2 - - + -
1076A GLU* 2.8 54.4 + - + +
1077A PHE* 3.0 31.0 + - + +
1092A ILE* 4.4 9.0 - - + -
1095A LEU* 3.9 27.8 - - + -
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Residues in contact with VAL1067 (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* 4.7 3.1 - - + -
1029A PHE 2.9 7.2 + - - +
1030A LEU* 3.4 23.2 - - + +
1031A ILE* 2.9 27.2 + - - +
1066A LEU* 1.3 83.3 - - - +
1068A GLN* 1.3 73.7 + - - +
1073A THR* 4.3 3.8 - - - -
1074A ARG 3.6 15.7 - - - +
1075A PRO* 4.1 10.5 - - + -
1077A PHE 5.2 1.3 - - - +
1111A PHE* 4.2 17.0 - - + -
1112A VAL* 4.5 6.7 - - + -
1116A ILE* 4.0 33.9 - - + -
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Residues in contact with GLN1068 (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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1031A ILE* 3.2 14.8 - - + +
1033A GLY* 3.5 13.6 - - - -
1041A PHE* 3.7 24.1 - - + -
1066A LEU* 4.3 8.1 - - + -
1067A VAL* 1.3 78.0 - - - +
1069A TYR* 1.3 65.0 + - - +
1073A THR* 3.5 1.0 - - - -
1074A ARG* 2.8 39.0 + - + +
1076A GLU* 2.8 33.2 + - + +
1095A LEU* 4.6 4.2 - - - +
1096A THR 2.8 22.2 + - - -
1098A LEU* 2.9 34.6 + - + +
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Residues in contact with TYR1069 (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* 3.5 34.1 - - + -
1031A ILE 3.0 15.7 + - - -
1032A ASP* 3.4 24.1 - - + +
1033A GLY 2.8 27.5 + - - -
1034A SER 3.8 0.7 + - - -
1068A GLN* 1.3 78.7 - - - +
1070A SER* 1.3 68.5 + - - +
1072A ARG 3.2 10.8 - - - +
1073A THR* 4.0 5.4 - - + -
1098A LEU* 3.7 5.6 - - - -
1103A PRO* 3.6 15.5 - - + -
1104A ASN 3.8 6.7 - - - -
1105A THR* 2.7 45.9 + - + +
1108A ALA* 3.4 24.9 - - + -
1135A VAL* 4.4 3.3 - - + +
1136A LEU 4.3 0.8 + - - -
1137A THR* 3.5 22.0 + - - +
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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