Contacts of the strand formed by residues 113 - 118 (chain B) in PDB entry 3DVA
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 THR 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B PRO 3.0 7.9 + - - -
77B VAL* 3.1 21.9 - - + +
78B PRO* 3.0 19.7 - - - +
111B PRO 4.3 0.7 + - - -
112B ILE* 1.3 74.1 + - - +
114B ILE* 1.3 63.8 + - - +
115B ARG* 4.8 0.9 - - + -
157B LEU* 4.2 18.4 - - + -
160B ALA* 2.9 46.4 + - + +
161B ILE* 3.3 16.2 + - + -
167B VAL* 3.4 9.9 - - - +
169B PHE* 4.3 10.1 - - + -
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Residues in contact with ILE 114 (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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63B GLY* 6.2 1.6 - - - -
78B PRO* 3.6 18.4 - - + +
80B ILE* 3.6 34.3 - - + -
83B PHE* 5.8 0.4 - - + -
89B VAL* 6.1 0.4 - - + -
93B ILE* 3.8 35.2 - - + -
97B MET* 3.8 23.8 - - + -
112B ILE* 3.9 13.0 - - + +
113B THR* 1.3 73.9 - - - +
115B ARG* 1.3 64.2 + - - +
116B SER* 5.0 2.2 - - - -
166B PRO* 6.3 0.4 - - + -
167B VAL 3.0 10.5 + - - +
168B ILE* 3.7 17.4 - - + +
169B PHE 2.8 32.3 + - - +
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Residues in contact with ARG 115 (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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9B ILE* 3.7 8.2 - - - +
13B LEU* 4.0 29.6 - - - +
25B ILE* 5.3 3.6 - - - +
39B ALA* 3.2 29.5 - - - +
40B THR* 4.2 11.3 - - - +
77B VAL* 4.4 14.7 + - + +
78B PRO 3.0 10.9 + - - +
79B GLU* 2.7 40.3 + - - +
80B ILE 3.0 22.2 + - - -
113B THR* 3.7 1.1 + - + -
114B ILE* 1.3 76.2 - - - +
116B SER* 1.3 66.0 + - - +
117B PRO* 5.8 1.2 - - - +
157B LEU* 4.4 9.9 - - + -
169B PHE* 3.4 13.9 - - + -
171B GLU* 2.7 38.8 + - - +
176B TYR* 4.2 3.0 + - - -
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Residues in contact with SER 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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80B ILE* 2.8 23.3 + - - +
82B PHE 3.5 0.2 - - - -
83B PHE* 3.0 49.1 + - - -
114B ILE* 5.0 2.0 - - - -
115B ARG* 1.3 79.7 - - - +
117B PRO* 1.3 67.4 - - - +
169B PHE 3.0 7.3 + - - -
170B LEU* 3.2 14.5 - - - +
171B GLU* 2.9 25.7 + - - -
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Residues in contact with PRO 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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36B VAL* 5.8 0.2 - - + -
37B PHE* 4.4 8.1 - - + -
79B GLU* 5.2 7.4 - - + +
80B ILE 3.5 5.6 - - - +
81B GLN* 2.9 29.6 - - - +
82B PHE* 3.7 8.9 - - + -
83B PHE* 3.0 25.3 + - - +
115B ARG* 4.8 1.8 - - - +
116B SER* 1.3 85.5 - - - +
118B PHE* 1.3 60.5 + - - +
128B HIS 4.3 2.2 - - - +
171B GLU* 2.9 16.6 - - - +
173B LEU* 3.6 20.0 - - + -
176B TYR* 3.5 20.4 - - + +
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Residues in contact with PHE 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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83B PHE* 4.4 11.9 - + + -
116B SER 4.4 0.2 - - - -
117B PRO* 1.3 75.6 - - - +
119B GLY* 1.3 74.7 + - - +
128B HIS 4.0 11.7 - - - +
129B SER* 4.5 0.2 - - - -
130B ASP 3.7 17.3 - - - +
131B SER* 3.8 24.9 - - - -
133B GLU* 4.5 8.3 - - - -
146B ILE* 3.8 24.7 - - + -
170B LEU* 3.6 36.6 - - + -
171B GLU 3.0 10.4 + - - -
172B HIS* 3.3 41.5 - + + -
173B LEU* 2.7 34.1 + - - +
209B TYR* 5.8 3.1 - + - -
210B GLY* 5.1 3.1 - - - -
261B GLU* 5.2 2.5 - - + -
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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