Contacts of the strand formed by residues 1011 - 1019 (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 ILE1011 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009B GLN 3.6 2.7 + - - +
1010B LYS* 1.4 71.3 - - - +
1012B LYS* 1.3 61.0 + - - +
1070B LEU* 4.0 23.6 - - + -
1110B PHE* 3.6 0.7 - - - -
1111B PHE* 2.9 48.4 + - + +
1112B GLU 4.5 2.5 - - - +
1113B TRP* 4.1 31.9 - - + -
1120B PRO* 4.4 7.9 - - + -
1140B LEU* 4.9 3.8 - - + -
1141B GLU 3.6 10.3 - - - +
1142B ASP* 3.5 20.9 - - - +
1143B ILE* 3.6 27.4 - - + -
1144B PRO* 3.8 11.4 - - + -
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Residues in contact with LYS1012 (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* 1.3 74.3 - - - +
1013B GLY* 1.3 65.4 + - - +
1014B THR* 4.7 4.5 - - - +
1094B LEU* 6.4 2.2 - - - -
1108B SER* 4.9 2.7 - - - +
1109B ILE 3.3 5.8 - - - +
1110B PHE* 3.5 37.2 - - + -
1111B PHE* 4.2 4.0 - - - -
1140B LEU* 3.0 10.4 - - - +
1141B GLU* 2.8 63.8 + - + +
1142B ASP* 2.9 28.6 + - - +
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Residues in contact with GLY1013 (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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1012B LYS* 1.3 79.7 - - - +
1014B THR* 1.3 65.4 + - - -
1015B VAL* 5.2 0.9 - - - -
1094B LEU* 5.6 0.2 - - - +
1108B SER* 3.6 7.4 + - - -
1109B ILE* 2.7 48.8 + - - -
1111B PHE* 4.0 5.8 - - - -
1138B VAL* 5.2 0.2 - - - -
1139B LYS 3.2 8.5 - - - -
1140B LEU* 4.2 6.1 - - - -
1141B GLU* 4.1 0.7 - - - -
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Residues in contact with THR1014 (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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1012B LYS* 4.7 4.3 - - - -
1013B GLY* 1.3 72.7 + - - -
1015B VAL* 1.3 60.4 + - - +
1016B VAL* 3.8 7.6 - - + -
1094B LEU* 4.4 21.0 - - + +
1098B PRO* 5.7 4.7 - - + -
1106B ALA* 4.7 7.6 - - + -
1107B PHE 3.6 3.8 - - - +
1108B SER* 5.0 0.2 - - - +
1137B SER 3.5 2.3 - - - +
1138B VAL* 3.3 7.1 - - - -
1139B LYS* 2.9 53.2 + - + +
1141B GLU* 3.1 24.3 + - - -
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Residues in contact with VAL1015 (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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1014B THR* 1.3 74.5 - - - +
1016B VAL* 1.3 61.1 + - - +
1017B LEU* 3.6 25.6 - - + +
1066B ILE* 5.6 1.6 - - + -
1068B MET* 3.9 13.9 - - - -
1090B LEU* 3.9 17.3 - - + -
1106B ALA* 3.7 1.0 - - - -
1107B PHE* 2.7 42.5 + - + +
1109B ILE* 3.7 25.8 - - + -
1125B ILE* 5.3 4.5 - - + -
1135B LEU* 4.0 16.6 - - + -
1137B SER 3.7 2.5 - - - -
1138B VAL* 3.7 20.6 - - + -
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Residues in contact with VAL1016 (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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1014B THR* 4.6 2.7 - - + -
1015B VAL* 1.3 71.3 - - - +
1017B LEU* 1.3 63.0 + - - +
1100B LEU 5.2 5.2 - - - +
1104B GLN* 3.5 43.1 - - + +
1105B ASP 4.0 7.0 - - - +
1106B ALA* 4.5 13.9 - - + +
1135B LEU* 3.3 6.8 - - - +
1136B VAL* 2.9 26.3 + - + -
1137B SER* 2.9 24.7 + - - +
1139B LYS* 3.1 29.8 - - - +
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Residues in contact with LEU1017 (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* 3.6 26.7 - - + +
1016B VAL* 1.3 76.3 - - - +
1018B MET* 1.3 64.6 + - - +
1019B PRO* 4.4 2.2 - - + +
1061B PHE* 3.7 39.7 - - + -
1066B ILE* 4.3 17.7 - - + -
1090B LEU* 4.4 1.6 - - + -
1104B GLN* 3.5 3.5 - - - -
1105B ASP* 3.1 32.0 + - + +
1107B PHE* 3.7 25.6 - - + -
1133B PHE* 4.1 12.1 - - + -
1134B PHE 3.2 12.6 - - - +
1135B LEU* 3.9 9.9 - - + -
1136B VAL* 3.8 2.9 - - - -
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Residues in contact with MET1018 (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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1017B LEU* 1.3 72.4 - - - +
1019B PRO* 1.3 66.8 - - + +
1022B VAL* 5.5 3.6 - - + -
1023B LEU* 3.8 35.7 - - + -
1103B ARG* 4.0 22.0 - - - +
1104B GLN* 3.4 46.7 - - + +
1133B PHE* 3.5 4.0 - - - -
1134B PHE* 2.6 63.4 + - + +
1136B VAL* 3.7 17.0 - - + -
1272B LEU* 5.0 7.2 - - + -
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Residues in contact with PRO1019 (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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1017B LEU* 4.4 2.9 - - + +
1018B MET* 1.3 91.4 - - + +
1020B LYS* 1.3 90.1 + - + +
1021B ASN* 3.4 1.8 - - + +
1022B VAL* 3.4 30.4 + - + +
1023B LEU* 4.1 4.3 + - - +
1058B ALA* 5.6 4.3 - - + -
1061B PHE* 3.6 30.3 - - + -
1103B ARG 4.7 2.9 - - - +
1105B ASP* 3.8 25.1 - - - +
1133B PHE* 4.4 2.7 - - + -
1156B TRP* 4.6 0.4 - - - -
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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