Contacts of the strand formed by residues 113 - 122 (chain B) in PDB entry 4J15
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 ILE 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ASP* 5.5 0.4 - - - +
462A GLY 4.9 0.2 - - - -
463A ALA 3.5 13.5 - - - +
464A PRO* 3.5 37.5 - - + -
63B ARG* 3.7 23.6 - - + -
64B ALA* 3.2 10.8 - - - +
65B ARG* 3.8 37.0 - - + +
112B SER* 1.3 75.3 - - - +
114B VAL* 1.3 61.5 - - - +
144B VAL* 3.5 5.5 - - - +
145B ILE* 2.9 46.0 + - + -
146B SER* 2.9 14.4 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL 3.8 0.9 - - - +
63B ARG* 3.4 5.0 - - - +
64B ALA 2.8 40.3 + - - +
66B VAL* 4.0 20.2 - - + -
80B LEU* 4.0 19.3 - - + -
108B ILE* 4.0 13.5 - - + -
113B ILE* 1.3 79.2 - - - +
115B ASP* 1.3 61.7 + - - +
116B VAL* 3.8 19.1 - - + -
142B ILE* 4.0 24.9 - - + -
143B TYR 2.9 13.7 - - - +
144B VAL* 4.0 9.2 - - + -
145B ILE* 4.7 1.1 - - - -
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TYR* 2.7 19.2 + - - -
45B LEU* 4.6 3.7 - - - +
61B TRP* 4.2 14.8 - - + -
62B VAL 3.5 2.7 - - - -
63B ARG* 2.8 45.3 + - - +
114B VAL* 1.3 70.7 - - - +
116B VAL* 1.3 60.5 + - - +
141B LYS 4.0 0.3 - - - +
142B ILE* 3.5 2.4 - - - -
143B TYR* 2.8 36.0 + - + +
145B ILE* 3.5 13.1 - - + +
603B GOL 2.5 33.4 + - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL 3.7 0.9 - - - +
61B TRP* 3.3 7.2 - - - -
62B VAL* 2.7 44.2 + - + +
78B LEU* 6.4 0.4 - - + -
80B LEU* 4.1 18.4 - - + -
114B VAL* 3.8 24.0 - - + -
115B ASP* 1.3 77.7 - - - +
117B GLU* 1.3 74.2 + - - +
137B LEU* 3.9 22.6 - - + +
139B VAL* 3.9 18.4 - - + -
141B LYS 3.3 7.9 - - - +
142B ILE* 3.8 21.1 - - + -
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Residues in contact with GLU 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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28B ARG* 4.5 1.2 + - - -
59B VAL* 3.7 24.8 - - + +
60B VAL 3.4 11.7 - - - +
61B TRP* 3.5 43.4 + - + +
116B VAL* 1.3 76.6 - - - +
118B GLY* 1.3 55.7 + - - +
139B VAL* 3.5 3.5 - - - -
140B GLN* 2.6 43.0 + - - +
141B LYS* 2.8 50.0 + - + +
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Residues in contact with GLY 118 (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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59B VAL* 3.4 5.5 - - - +
60B VAL* 2.9 34.6 + - - +
116B VAL* 4.2 1.2 - - - +
117B GLU* 1.3 77.2 - - - +
119B VAL* 1.3 64.2 + - - -
137B LEU* 3.9 11.7 - - - +
138B HIS 3.0 17.3 - - - -
139B VAL* 4.1 1.1 - - - -
140B GLN* 3.8 6.1 - - - -
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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
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57B ASP* 3.6 17.3 - - - +
58B GLU 3.3 12.6 - - - +
59B VAL* 4.4 6.7 - - + +
118B GLY* 1.3 73.1 - - - -
120B VAL* 1.3 66.9 + - - +
121B ARG* 3.6 44.3 + - + +
137B LEU* 3.5 4.8 - - - -
138B HIS* 2.9 38.0 + - + +
140B GLN* 2.7 35.7 - - + +
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Residues in contact with VAL 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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51B LEU* 4.2 14.6 - - + -
52B THR 4.0 9.4 - - - +
55B LYS* 3.3 33.0 - - + +
56B ALA* 4.1 1.1 - - - -
57B ASP* 2.6 30.3 + - - -
58B GLU 2.9 12.7 + - - +
60B VAL* 4.0 24.9 - - + -
119B VAL* 1.3 73.0 - - - +
121B ARG* 1.3 63.7 + - - +
122B LYS 4.3 0.2 - - - -
135B VAL* 3.7 35.9 - - + -
136B GLU 3.8 3.8 - - - +
137B LEU* 4.3 4.3 - - + -
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Residues in contact with ARG 121 (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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57B ASP* 2.6 42.4 + - - +
119B VAL* 3.6 34.0 - - + +
120B VAL* 1.3 76.3 - - - +
122B LYS* 1.3 68.5 + - - +
123B VAL* 3.3 2.8 + - + +
135B VAL* 3.2 6.1 - - - -
136B GLU* 2.9 39.3 + - + +
138B HIS* 3.5 43.2 + - + +
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Residues in contact with LYS 122 (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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53B ILE* 3.7 29.9 - - + +
56B ALA* 4.7 12.1 - - + +
57B ASP* 5.4 1.2 + - - -
120B VAL 4.3 0.8 + - - -
121B ARG* 1.3 75.7 - - - +
123B VAL* 1.3 66.9 + - - +
124B ASN* 3.4 27.3 + - - +
134B ASP 3.6 7.0 - - - +
135B VAL* 4.3 2.4 - - - +
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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