Contacts of the strand formed by residues 116 - 120 (chain B) in PDB entry 2IIK
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 LEU 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ARG* 3.3 12.8 + - - +
414A MET* 3.3 25.9 - - + +
69B MET* 5.4 1.8 - - - -
86B ILE* 3.2 33.9 - - + +
88B VAL* 4.1 3.6 - - + -
98B ALA* 3.9 15.9 - - + +
101B ALA* 3.4 49.6 - - + +
102B ARG* 3.9 13.2 - - + +
105B GLN* 3.7 19.5 - - + +
114B VAL 4.1 0.2 + - - -
115B PRO* 1.3 76.3 - - - +
117B SER* 1.3 77.7 + - - +
118B THR* 4.3 2.2 - - + -
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 5.9 0.4 - - - +
120A ASN 3.5 14.6 - - - -
121A ARG* 3.7 31.5 + - - -
128A GLN* 4.8 9.9 + - - +
85B ASP* 5.1 1.0 + - - -
86B ILE 2.9 7.8 + - - +
87B CYS* 3.4 18.2 - - - +
88B VAL 3.0 22.5 + - - -
98B ALA* 5.8 0.4 - - - -
116B LEU* 1.3 81.3 - - - +
118B THR* 1.3 70.0 + - - +
119B VAL* 4.7 1.6 - - - +
132B SER* 5.3 0.9 + - - -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 3.5 2.6 - - - +
120A ASN* 2.9 40.5 + - - +
88B VAL* 3.1 15.0 - - + +
90B ASN* 5.5 0.2 - - + -
95B GLY 3.4 14.9 + - - -
96B ALA* 3.1 31.7 + - - +
97B GLY 3.6 4.9 - - - +
98B ALA* 3.4 25.0 + - - +
101B ALA* 4.0 13.0 - - + -
116B LEU* 4.3 0.4 - - + -
117B SER* 1.3 79.7 + - - +
119B VAL* 1.3 70.5 + - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 6.0 0.4 - - - +
118A THR 3.5 7.9 - - - +
119A VAL* 4.0 16.4 - - + +
87B CYS* 3.3 24.2 - - - -
88B VAL 2.9 7.3 + - - +
89B GLY* 3.5 9.4 - - - -
90B ASN 3.1 24.2 + - - +
96B ALA* 4.7 2.7 - - - -
117B SER* 4.7 2.9 - - - +
118B THR* 1.3 81.1 - - - +
120B ASN* 1.3 61.2 + - - +
125B SER* 3.7 23.4 - - - +
128B GLN* 4.1 15.7 - - + +
129B ALA* 3.9 12.8 - - - +
132B SER* 4.5 11.2 - - - +
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Residues in contact with ASN 120 (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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95A GLY* 2.5 37.6 + - - +
98A ALA* 3.6 20.3 - - - +
117A SER* 3.5 3.6 - - - -
118A THR* 2.9 46.4 + - - +
90B ASN 3.6 10.8 - - - +
91B VAL* 3.4 16.7 + - - +
96B ALA* 4.3 3.8 - - + +
119B VAL* 1.3 73.8 - - - +
121B ARG* 1.3 57.1 + - - +
122B GLN* 2.8 37.5 + - - +
125B SER* 3.4 4.2 + - - -
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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