Contacts of the strand formed by residues 30 - 35 (chain D) in PDB entry 3GV5
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 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D ARG* 4.1 14.8 - - + +
29D VAL* 1.3 76.6 - - - +
31D VAL* 1.3 73.9 + - - +
129D PHE* 4.1 3.8 - - + -
130D VAL 3.6 4.0 - - - +
131D ASP* 3.7 34.1 - - - +
198D GLY 3.7 0.7 - - - +
199D VAL* 3.3 5.7 - - - +
200D ALA 2.8 36.4 + - - +
201D SER 4.2 4.9 - - - +
202D ASN* 3.8 27.4 - - - +
203D LYS* 4.0 21.5 - - + +
206D ALA* 3.7 14.4 - - + +
293D VAL* 3.7 17.9 - - + -
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Residues in contact with VAL 31 (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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29D VAL 4.2 0.4 + - - -
30D ILE* 1.3 80.6 - - - +
32D HIS* 1.3 71.7 + - - +
33D VAL* 4.1 7.6 - - + -
128D ASN 3.9 0.5 - - - +
129D PHE* 3.3 5.4 - - - -
130D VAL* 3.0 63.2 + - + +
132D LEU* 3.7 25.5 - - + +
180D ALA* 3.8 26.2 - - + -
183D MSE 4.0 7.9 - - - -
197D ALA* 4.0 7.4 - - + -
198D GLY 3.2 10.5 - - - +
199D VAL* 4.0 4.5 - - + -
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Residues in contact with HIS 32 (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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31D VAL* 1.3 71.0 - - - +
33D VAL* 1.3 60.6 + - - +
34D ASP* 3.5 28.2 - - + +
127D GLU* 2.8 35.9 + - + +
128D ASN 3.5 9.4 - - - -
129D PHE* 3.5 31.2 - + + -
197D ALA* 3.1 5.9 - - - -
198D GLY 2.8 31.7 + - - -
206D ALA* 3.5 25.1 - - + +
207D LYS* 3.7 20.2 - - + +
210D SER* 2.8 23.6 + - - -
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Residues in contact with VAL 33 (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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31D VAL* 4.1 22.0 - - + -
32D HIS* 1.3 76.6 + - - +
34D ASP* 1.3 61.9 + - - +
35D LEU* 4.0 12.1 - - + -
109D VAL* 5.3 1.6 - - + -
113D LEU* 4.3 27.8 - - + -
126D ASP 3.7 0.9 - - - +
127D GLU* 3.2 6.9 - - - +
128D ASN* 2.9 38.2 + - + +
130D VAL* 5.2 1.6 - - + -
183D MSE 4.6 9.0 - - + -
184D ARG* 5.4 4.9 - - + -
187D MSE 3.6 29.2 - - - -
195D GLY 5.8 0.4 - - - -
196D CYS 3.5 8.5 - - - +
197D ALA* 4.7 5.8 - - + -
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Residues in contact with ASP 34 (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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32D HIS* 3.5 21.2 - - + +
33D VAL* 1.3 75.6 - - - +
35D LEU* 1.3 60.9 + - - +
36D ASP* 3.8 0.7 + - - +
126D ASP* 3.4 5.5 - - - +
127D GLU* 3.2 9.8 - - - +
196D CYS* 2.7 47.0 + - + +
207D LYS* 5.2 0.7 + - - -
210D SER* 4.4 6.3 + - - +
211D GLY* 6.1 0.9 - - - -
421D CA 2.3 31.9 - - - -
422D CA 2.6 22.6 - - - -
424D ADI 3.5 3.6 + - - -
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Residues in contact with LEU 35 (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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33D VAL* 4.0 14.1 - - + -
34D ASP* 1.3 79.3 + - - +
36D ASP* 1.3 61.6 + - - +
38D PHE* 4.0 20.2 - - + -
41D GLN* 4.3 1.1 - - - +
109D VAL* 4.5 9.9 - - + -
126D ASP* 2.9 26.7 + - + +
128D ASN* 6.3 0.2 - - - +
187D MSE 3.0 32.1 - - + -
193D LEU* 3.5 46.0 - - + -
194D THR 3.7 7.4 - - - +
195D GLY* 4.1 5.6 - - - -
421D CA 2.3 30.7 - - - -
424D ADI 3.3 0.9 + - - -
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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