Contacts of the strand formed by residues 113 - 118 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D PRO 2.9 9.7 + - - -
77D VAL* 3.2 34.9 - - + +
78D PRO* 3.3 4.2 - - - +
111D PRO 4.3 0.5 + - - -
112D ILE* 1.3 72.9 + - - +
114D ILE* 1.3 64.1 + - - +
115D ARG* 4.7 0.9 - - + -
157D LEU* 4.0 18.8 - - + -
160D ALA* 2.8 48.9 + - + -
161D ILE* 3.2 15.3 + - + -
167D VAL* 3.3 8.2 - - - +
169D PHE* 4.3 10.8 - - + -
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLY* 6.4 0.4 - - - -
78D PRO* 3.7 17.3 - - + +
80D ILE* 3.6 33.4 - - + -
93D ILE* 3.7 28.7 - - + -
97D MET* 3.7 29.4 - - + -
112D ILE* 4.0 13.9 - - + -
113D THR* 1.3 72.4 - - - +
115D ARG* 1.3 63.0 + - - +
116D SER* 4.9 2.5 - - - -
142D LEU* 6.3 0.2 - - + -
166D PRO* 6.2 0.9 - - + -
167D VAL 2.8 13.8 + - - +
168D ILE* 3.6 18.0 - - + +
169D PHE* 2.7 33.4 + - - +
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 4.0 6.1 - - - +
13D LEU* 4.1 28.9 - - - +
25D ILE* 5.4 3.6 - - - +
39D ALA* 3.3 28.0 - - - +
40D THR* 4.3 12.3 - - - +
77D VAL* 4.3 17.2 + - + -
78D PRO 3.1 10.9 + - - +
79D GLU* 2.7 41.0 + - - +
80D ILE 3.0 24.8 + - - +
113D THR* 3.6 1.3 + - + -
114D ILE* 1.3 73.9 - - - +
116D SER* 1.3 62.1 + - - +
117D PRO* 5.8 2.6 - - - +
157D LEU* 4.4 10.1 - - + -
169D PHE* 3.5 14.1 - - + -
171D GLU* 2.7 39.2 + - - +
176D TYR* 4.3 2.8 + - - -
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D ILE* 2.8 23.7 + - - +
82D PHE 3.4 0.5 - - - -
83D PHE* 3.0 47.4 + - - -
114D ILE* 4.9 2.2 - - - -
115D ARG* 1.3 78.9 - - - +
117D PRO* 1.3 68.4 - - - +
118D PHE 4.0 0.2 + - - -
169D PHE 3.1 7.1 + - - -
170D LEU* 3.4 14.1 - - - +
171D GLU* 3.0 23.1 + - - -
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Residues in contact with PRO 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.2 15.7 - - + -
79D GLU* 5.2 7.4 - - + +
80D ILE 3.5 5.4 - - - +
81D GLN* 2.9 29.8 - - - +
82D PHE* 3.6 5.6 - - + +
83D PHE 2.9 25.3 + - - -
115D ARG* 4.8 1.3 - - - +
116D SER* 1.3 84.6 - - - +
118D PHE* 1.3 61.7 + - - +
128D HIS 4.2 2.0 - - - +
171D GLU* 2.9 15.0 - - - +
173D LEU* 3.5 18.8 - - + -
176D TYR* 3.5 20.2 - - + +
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Residues in contact with PHE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 4.3 12.8 - + + -
116D SER 4.5 0.2 - - - -
117D PRO* 1.3 75.6 - - - +
119D GLY* 1.3 69.0 + - - +
128D HIS 3.9 10.5 - - - +
130D ASP 3.7 16.2 - - - +
131D SER* 3.5 27.8 - - - -
132D LEU 5.6 0.4 - - - +
133D GLU* 4.3 10.3 - - - -
146D ILE* 3.7 27.1 - - + -
170D LEU* 3.7 32.3 - - + -
171D GLU 3.0 11.7 + - - -
172D HIS* 3.3 42.2 - + + -
173D LEU* 2.6 34.6 + - - +
209D TYR* 5.6 2.9 - + - -
210D GLY* 4.9 2.9 - - - -
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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