Contacts of the strand formed by residues 127 - 131 (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 GLU 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D HIS* 2.8 33.3 + - - +
33D VAL 3.2 3.4 - - - -
34D ASP* 3.2 14.5 - - - +
122D ARG* 3.7 2.8 + - - +
123D LEU* 2.8 49.3 + - - +
124D GLY 4.3 2.4 - - - +
125D PHE 5.1 0.5 - - - -
126D ASP* 1.3 87.2 - - - +
128D ASN* 1.3 66.4 + - - +
207D LYS* 2.8 20.0 + - - -
422D CA 2.1 30.6 - - - -
873E G 3.2 24.4 - - - +
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Residues in contact with ASN 128 (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 3.9 0.3 - - - +
32D HIS* 3.5 3.8 - - - -
33D VAL* 2.9 36.8 + - + +
35D LEU* 6.3 0.2 - - - +
106D SER 5.3 0.4 + - - -
109D VAL* 3.7 18.6 - - - +
110D THR* 2.9 27.0 + - - +
113D LEU* 3.4 34.7 - - + +
120D VAL* 3.5 17.9 - - + +
121D GLU 3.2 6.1 - - - -
122D ARG* 3.8 7.8 - - - +
125D PHE 5.8 1.0 + - - -
126D ASP 4.9 2.6 + - - -
127D GLU* 1.3 84.3 + - - +
129D PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 129 (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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30D ILE* 4.1 5.2 - - + -
31D VAL 3.3 11.7 - - - +
32D HIS* 3.5 31.9 - + + -
120D VAL* 3.3 6.4 - - - +
121D GLU* 2.8 50.3 + - + +
123D LEU* 3.9 26.5 - - + -
128D ASN* 1.3 75.5 - - - +
130D VAL* 1.3 62.0 + - - +
203D LYS* 3.4 58.3 - - + -
207D LYS* 3.9 19.1 - - + -
293D VAL* 3.6 21.8 - - + +
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Residues in contact with VAL 130 (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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30D ILE* 3.6 3.3 - - - +
31D VAL* 3.0 45.6 + - + +
33D VAL* 5.2 1.3 - - + -
113D LEU* 4.3 16.8 - - + +
117D SER* 3.4 33.0 - - - +
119D VAL 3.8 9.6 - - - +
120D VAL* 4.0 19.5 - - + -
128D ASN* 5.1 1.3 - - + +
129D PHE* 1.3 80.3 - - - +
131D ASP* 1.3 61.6 + - - +
132D LEU* 3.4 14.3 + - + -
183D MSE 3.9 18.4 - - + -
293D VAL* 4.5 4.5 - - - -
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Residues in contact with ASP 131 (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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28D ARG* 3.9 15.6 + - - +
29D VAL 3.7 0.5 - - - +
30D ILE* 3.7 23.2 - - + +
117D SER* 3.8 16.3 + - - -
119D VAL* 3.7 21.6 + - + +
130D VAL* 1.3 72.5 - - - +
132D LEU* 1.3 59.4 + - - +
133D THR* 2.6 33.3 + - - -
134D GLU* 4.8 3.5 + - - +
293D VAL* 4.1 18.6 + - + +
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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