Contacts of the strand formed by residues 113 - 117 (chain B) in PDB entry 5KM2
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 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MET* 5.6 1.6 - - - -
52B PHE 3.8 0.2 - - - +
53B LEU* 3.2 6.2 - - - -
54B VAL* 2.9 45.0 + - + +
77B LEU* 3.5 40.8 - - + +
78B MET* 3.8 22.2 - - + +
96B MET* 3.9 35.4 - - + -
97B VAL 3.6 7.0 - - - +
98B VAL* 3.7 23.6 - - + -
112B HIS* 1.3 72.5 - - - +
114B HIS* 1.3 65.1 + - - +
115B VAL* 4.4 7.8 - - + +
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 3.5 31.2 - + - -
43B ASP* 3.9 6.3 - - - -
51B HIS* 3.0 21.7 + - - +
52B PHE 3.5 4.0 - - - -
53B LEU* 3.3 17.8 - - + +
96B MET* 3.1 8.1 - - - +
97B VAL* 2.8 47.9 + - + +
99B ASN* 4.3 7.4 - - - -
107B SER* 5.5 1.6 - - - -
112B HIS* 3.3 26.1 - + - -
113B LEU* 1.3 73.5 - - - +
115B VAL* 1.3 62.2 + - - +
116B LEU* 3.9 17.7 - - + -
201B CL 3.3 16.7 - - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.8 0.7 - - - +
51B HIS* 3.3 3.8 - - - -
52B PHE* 2.8 82.0 + - + +
54B VAL* 4.6 0.9 - - + -
81B GLY* 4.4 6.5 - - - +
85B ALA* 4.4 6.1 - - + -
90B LEU* 4.8 2.0 - - + -
94B TYR* 4.0 31.6 - - + -
95B ARG 3.4 3.1 - - - +
96B MET* 4.2 20.4 - - + -
113B LEU* 4.4 10.5 - - + +
114B HIS* 1.3 79.9 - - - +
116B LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 4.0 20.4 - - + -
47B GLN* 3.8 17.5 - - + -
48B ALA* 4.1 9.0 - - + -
50B THR 3.3 4.5 - - - -
51B HIS* 3.6 34.3 - - + +
90B LEU* 4.8 1.3 - - - -
94B TYR* 3.2 6.6 - - - +
95B ARG* 2.8 47.5 + - + +
97B VAL* 4.0 16.2 - - + -
114B HIS* 3.9 22.9 - - + -
115B VAL* 1.3 75.2 - - - +
117B GLY* 1.3 57.4 + - - +
121B MET* 3.9 25.2 - - + +
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Residues in contact with GLY 117 (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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103A ASP* 5.6 0.2 - - - -
48B ALA* 3.4 11.7 - - - +
49B PRO* 3.5 0.3 - - - +
50B THR 2.9 30.6 + - - +
90B LEU* 4.2 17.2 - - - +
93B GLY 4.3 8.3 - - - -
94B TYR* 4.3 1.8 - - - -
116B LEU* 1.3 75.4 - - - +
118B GLY* 1.3 59.4 + - - -
119B ARG* 3.2 12.1 - - - -
121B MET* 4.8 2.2 - - - -
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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
------------------------------------------------------------
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