Contacts of the strand formed by residues 1120 - 1127 (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 PRO1120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B ILE* 4.4 8.5 - - + -
1070B LEU* 3.6 29.4 - - + -
1071B ILE 3.1 13.7 - - - +
1113B TRP* 4.9 0.9 - - + -
1117B PHE* 3.9 10.0 - - + -
1118B GLY 3.3 10.1 - - - +
1119B ILE* 1.3 86.0 - - + +
1121B GLY* 1.3 58.9 + - - +
1122B ALA 3.7 2.5 - - - +
1140B LEU* 3.7 26.5 - - + -
1143B ILE* 4.2 8.7 - - + -
1149B ILE* 3.3 36.5 - - + +
1151B PHE* 4.5 1.3 - - + -
1171B VAL* 4.2 1.0 - - - +
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Residues in contact with GLY1121 (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 2.9 6.6 + - - -
1073B ALA* 3.7 21.8 - - - +
1119B ILE* 3.4 5.0 + - - -
1120B PRO* 1.3 72.2 - - - +
1122B ALA* 1.3 62.2 + - - +
1151B PHE* 4.1 0.9 - - - -
1170B PHE* 3.8 1.6 - - - -
1171B VAL* 3.3 40.5 + - - +
1184B LEU* 3.9 13.3 - - - +
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Residues in contact with ALA1122 (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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1070B LEU* 3.6 4.5 - - - +
1071B ILE* 2.9 40.8 + - + +
1120B PRO* 3.7 0.9 - - - +
1121B GLY* 1.3 78.2 + - - +
1123B PHE* 1.3 66.4 + - - +
1151B PHE* 3.8 10.2 - - - -
1168B ILE* 4.0 18.4 - - + -
1169B PHE 3.1 15.5 - - - +
1170B PHE* 4.2 14.8 - - + -
1184B LEU* 4.8 0.9 - - + -
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Residues in contact with PHE1123 (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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1068B MET* 3.6 29.4 - - + -
1069B GLN 3.4 11.2 - - - +
1070B LEU* 4.1 7.4 - - + -
1071B ILE* 3.6 7.9 - - - -
1122B ALA* 1.3 76.8 - - - +
1124B TYR* 1.3 69.6 + - - +
1125B ILE* 4.0 13.2 - - + -
1135B LEU* 4.1 4.3 - - + -
1138B VAL* 3.5 25.1 - - + -
1151B PHE* 3.3 52.3 - + + -
1153B CYS* 4.0 6.7 - - - -
1167B ARG 3.7 0.2 - - - +
1168B ILE* 3.2 4.7 - - - -
1169B PHE* 2.9 63.6 + + + -
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Residues in contact with TYR1124 (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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1068B MET* 3.0 25.8 - - - +
1069B GLN* 2.7 43.2 + - + +
1071B ILE* 3.6 14.8 - - + -
1084B VAL* 4.2 17.0 - - + -
1123B PHE* 1.3 75.4 - - - +
1125B ILE* 1.3 60.5 + - - +
1166B ASN* 4.2 27.1 - - + -
1167B ARG 3.2 6.5 - - - +
1168B ILE* 3.8 34.5 - - + -
1186B LYS* 4.8 2.4 + - - -
1187B TYR* 3.1 25.9 + + - -
1190B GLU* 3.9 11.9 + - - -
1191B GLU* 4.7 4.7 - - - -
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Residues in contact with ILE1125 (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* 5.3 2.2 - - + -
1066B ILE* 3.6 25.8 - - + -
1067B SER 3.2 15.7 - - - +
1068B MET* 3.9 15.7 - - + -
1123B PHE* 4.0 6.3 - - + -
1124B TYR* 1.3 75.9 - - - +
1126B LYS* 1.3 67.1 + - - +
1127B ASN 4.4 0.3 + - - -
1133B PHE* 4.0 15.5 - - + -
1135B LEU* 4.1 21.3 - - + -
1157B VAL* 4.4 10.4 - - + +
1158B TYR 5.7 0.2 - - - +
1167B ARG* 2.9 33.2 + - + +
1169B PHE* 3.3 37.5 - - + -
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Residues in contact with LYS1126 (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* 3.5 5.9 - - - +
1067B SER* 3.0 36.9 + - - +
1069B GLN* 3.9 19.7 - - - +
1087B GLU* 3.2 23.4 + - - -
1125B ILE* 1.3 82.4 - - - +
1127B ASN* 1.3 58.7 + - - +
1128B PHE* 3.4 23.3 + - + -
1160B PHE* 3.4 37.5 - - + -
1166B ASN* 3.5 37.2 - - + +
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Residues in contact with ASN1127 (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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1065B ASN 3.9 3.8 + - - -
1125B ILE 4.2 1.0 + - - -
1126B LYS* 1.3 70.4 - - - +
1128B PHE* 1.3 56.4 + - - +
1129B MET* 3.1 37.6 + - - +
1131B ASP 3.2 17.0 + - - +
1132B GLU* 3.7 1.6 - - - -
1133B PHE* 3.2 31.1 - - + -
1157B VAL* 3.1 26.0 - - + +
1158B TYR 3.3 22.8 + - - +
1159B ASN* 3.0 29.3 + - - -
1160B PHE* 3.5 5.0 + - - +
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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