Contacts of the strand formed by residues 113 - 118 (chain B) in PDB entry 3JT0
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 VAL 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.8 2.8 - - + +
59B ARG* 3.9 25.4 - - + -
60B LYS 3.5 9.0 - - - +
61B ILE* 3.9 7.6 - - + -
107B TRP* 3.3 46.7 - - + +
111B GLU* 3.8 14.4 - - + +
112B ASP* 1.3 78.8 - - - +
114B LYS* 1.3 69.8 + - - +
115B VAL* 4.4 7.0 - - + -
128B ARG 4.1 0.2 - - - +
129B SER* 3.2 3.9 - - - -
130B THR* 2.5 47.6 + - + +
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE 3.4 1.6 - - - +
59B ARG* 3.6 1.6 - - - -
60B LYS* 2.7 60.4 + - + +
113B VAL* 1.3 77.1 - - - +
115B VAL* 1.3 64.7 + - - +
116B ILE* 3.8 27.6 + - + +
124B GLU* 5.9 0.2 + - - -
127B GLN* 3.0 38.2 + - - +
128B ARG 3.4 5.8 - - - +
129B SER* 3.7 17.5 - - - +
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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
----------------------------------------------------------
30B ILE* 3.6 19.9 - - + +
33B ILE* 3.7 29.8 - - + -
40B ILE* 3.7 33.9 - - + -
57B MSE 4.0 24.2 - - + -
58B ILE 3.2 8.3 - - - +
59B ARG* 4.7 2.0 - - - -
113B VAL* 4.4 9.9 - - + -
114B LYS* 1.3 77.2 - - - +
116B ILE* 1.3 63.5 + - - +
127B GLN* 3.1 7.6 - - - +
128B ARG 2.8 32.9 + - - -
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Residues in contact with ILE 116 (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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56B GLU 3.5 2.1 - - - +
57B MSE 3.4 1.7 - - - -
58B ILE* 2.6 61.8 + - + +
60B LYS* 5.1 9.6 - - + -
114B LYS* 3.8 37.5 - - + +
115B VAL* 1.3 80.5 - - - +
117B LEU* 1.3 62.9 + - - +
118B LYS* 3.9 22.9 - - + -
124B GLU* 3.4 33.7 - - + +
126B ALA 4.0 5.2 - - - +
127B GLN* 4.3 4.9 - - + -
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Residues in contact with LEU 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 VAL* 3.4 35.7 - - + +
30B ILE* 4.4 13.6 - - + +
42B LEU* 3.9 22.9 - - + -
52B MSE 4.7 0.7 - - + -
55B TRP* 3.9 21.8 - - + -
56B GLU 3.4 14.4 - - - +
57B MSE 4.3 13.7 - - + +
70B TYR* 4.7 3.8 - - + -
115B VAL 4.2 0.6 + - - -
116B ILE* 1.3 73.2 - - - +
118B LYS* 1.3 69.3 + - - +
124B GLU* 3.3 5.7 - - - +
125B VAL* 2.9 43.9 + - + -
126B ALA 3.1 13.6 + - - +
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Residues in contact with LYS 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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55B TRP* 3.1 10.7 - - - +
56B GLU* 2.7 64.5 + - + +
58B ILE* 3.8 22.2 - - + +
116B ILE* 3.9 18.8 - - + -
117B LEU* 1.3 78.4 - - - +
119B ASN* 1.3 61.4 + - - +
122B GLY 4.3 14.6 + - - +
123B GLU 3.5 8.3 - - - +
124B GLU* 4.1 21.3 + - + +
125B VAL* 4.6 0.2 - - - -
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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