Contacts of the strand formed by residues 1066 - 1072 (chain B) in PDB entry 2IUK
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 ILE1066 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015B VAL* 5.6 2.7 - - + -
1017B LEU* 4.3 7.4 - - + -
1061B PHE* 3.5 48.6 + - + +
1064B ARG 3.8 0.4 - - - -
1065B ASN* 1.3 84.8 - - - +
1067B SER* 1.3 60.5 + - - +
1068B MET* 5.1 1.5 - - + +
1088B VAL 3.9 0.3 - - - +
1089B TYR* 3.4 3.8 - - - +
1090B LEU* 3.3 42.0 + - + +
1109B ILE* 4.8 0.9 - - - +
1125B ILE* 3.6 34.8 - - + -
1126B LYS 3.5 5.8 - - - +
1127B ASN* 4.6 1.6 - - - +
1129B MET* 4.6 1.3 - - - -
1133B PHE* 3.4 31.4 - - + -
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Residues in contact with SER1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066B ILE* 1.3 74.4 - - - +
1068B MET* 1.3 61.3 + - - +
1069B GLN* 4.1 1.7 + - - -
1087B GLU* 3.1 38.8 + - - +
1088B VAL 3.3 9.2 - - - -
1089B TYR* 3.9 12.6 - - - +
1125B ILE* 3.2 11.4 - - - +
1126B LYS* 3.0 46.6 + - - +
1128B PHE* 3.7 9.6 - - - -
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Residues in contact with MET1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015B VAL* 3.9 28.3 - - - -
1066B ILE* 5.1 2.9 - - + -
1067B SER* 1.3 81.0 - - - +
1069B GLN* 1.3 62.5 + - - +
1070B LEU* 4.4 4.7 - - + -
1086B LYS 3.5 1.6 - - - +
1087B GLU* 3.9 0.3 - - - -
1088B VAL* 3.0 31.3 + - - +
1090B LEU* 5.5 0.9 - - + -
1109B ILE* 4.5 6.7 - - + -
1111B PHE* 3.6 33.4 - - + -
1123B PHE* 3.6 37.2 - - + -
1124B TYR 3.0 11.4 - - - +
1125B ILE* 3.9 20.0 - - + -
1138B VAL* 4.0 17.0 - - + -
1140B LEU* 4.9 0.2 - - + -
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Residues in contact with GLN1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067B SER* 4.1 3.2 + - - -
1068B MET* 1.3 74.3 - - - +
1070B LEU* 1.3 61.8 + - - +
1071B ILE* 3.6 1.7 - - - +
1084B VAL* 3.8 11.9 - - + +
1085B GLY 3.7 20.5 - - - +
1086B LYS 3.9 10.8 - - - +
1087B GLU* 3.7 30.9 + - - +
1111B PHE* 5.4 0.9 - - - -
1123B PHE* 4.3 1.8 - - - -
1124B TYR* 2.7 61.9 + - + +
1126B LYS* 3.9 23.8 - - - +
1166B ASN* 4.8 2.2 + - - -
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Residues in contact with LEU1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B ILE* 4.0 19.1 - - + -
1068B MET* 4.4 6.3 - - + -
1069B GLN* 1.3 73.3 - - - +
1071B ILE* 1.3 60.2 + - - +
1084B VAL* 3.3 6.1 - - - +
1085B GLY* 3.0 28.4 + - - +
1086B LYS 5.2 0.2 + - - -
1111B PHE* 4.3 35.2 - - + -
1112B GLU 5.8 0.7 - - - +
1117B PHE* 3.4 20.9 - - + -
1120B PRO* 3.6 29.2 - - + -
1122B ALA 3.6 4.0 - - - +
1123B PHE* 4.1 15.5 - - + -
1140B LEU* 3.7 21.8 - - + -
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Residues in contact with ILE1071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069B GLN 3.6 17.0 - - - +
1070B LEU* 1.3 75.6 - - - +
1072B SER* 1.3 71.1 + - - +
1082B GLY* 4.2 2.2 - - - -
1083B LYS 3.6 3.4 - - - -
1084B VAL* 3.8 8.7 - - + -
1117B PHE* 3.8 1.8 - - - -
1120B PRO* 3.1 6.8 - - - +
1121B GLY 2.9 22.3 + - - -
1122B ALA* 2.9 19.3 + - + +
1123B PHE* 3.6 16.2 - - - +
1124B TYR* 3.6 28.0 - - + +
1168B ILE* 4.3 3.4 - - + -
1184B LEU* 3.7 12.8 - - + -
1187B TYR* 3.7 46.9 - - + -
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Residues in contact with SER1072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071B ILE* 1.3 75.3 - - - +
1073B ALA* 1.3 59.9 + - - +
1074B THR 3.4 1.7 + - - -
1075B GLN* 3.1 38.5 + - - +
1082B GLY* 3.3 14.5 - - - -
1083B LYS* 3.0 19.7 + - - -
1117B PHE* 3.8 13.8 - - - -
1118B GLY 3.7 13.5 + - - -
1119B ILE 3.5 8.9 + - - -
1183B PRO* 3.5 1.1 - - - +
1184B LEU* 3.1 17.4 - - - +
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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