Contacts of the strand formed by residues 134 - 140 (chain D) in PDB entry 2VM8
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 ASP 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D THR 3.8 7.6 + - - +
103D MET* 3.5 22.8 - - + -
104D ILE 3.5 2.6 + - - -
133D CYS* 1.3 83.0 - - - +
135D TYR* 1.3 62.1 + - - +
398D LYS* 3.1 23.9 + - - +
408D ASP* 4.7 1.9 + - - +
448D SER* 4.8 2.2 + - - -
449D GLN* 3.5 17.6 - - - +
467D ARG* 2.8 64.7 + - - +
469D ILE* 3.6 13.1 - - + +
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Residues in contact with TYR 135 (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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89D PHE* 5.0 0.7 - + - -
103D MET* 3.7 7.1 - - - +
104D ILE* 3.2 32.3 - - + +
124D ARG* 3.0 26.5 + - - -
127D ALA* 3.3 39.8 - - + +
128D ASP* 3.0 15.7 + - - -
131D SER* 4.4 9.4 - - - +
133D CYS 4.3 7.2 - - - +
134D ASP* 1.3 80.1 - - - +
136D SER* 1.3 66.9 + - - +
137D LEU* 3.9 15.9 - - + -
466D GLY 4.3 4.0 - - - -
467D ARG 2.8 24.9 + - - +
468D TYR* 3.4 35.8 - + + -
469D ILE* 2.6 35.9 + - - +
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Residues in contact with SER 136 (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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103D MET* 3.5 17.3 - - - -
104D ILE 3.1 6.7 + - - +
105D ILE* 3.4 8.5 - - - -
106D ASP 3.1 20.4 + - - -
135D TYR* 1.3 78.4 - - - +
137D LEU* 1.3 75.0 + - - +
468D TYR* 3.8 13.9 + - - -
469D ILE 2.6 24.5 + - - -
471D ARG* 3.0 26.3 + - - -
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Residues in contact with LEU 137 (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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89D PHE* 4.9 2.5 - - + -
105D ILE* 4.2 1.6 - - - -
106D ASP* 3.8 21.3 - - + -
108D VAL* 3.8 29.6 - - + -
120D PHE* 3.8 14.6 - - + -
123D TRP* 4.5 11.2 - - + +
124D ARG* 3.4 47.3 - - + +
135D TYR* 3.9 13.7 - - + -
136D SER* 1.3 88.9 + - - +
138D HIS* 1.3 60.5 + - - +
161D VAL* 4.0 9.9 - - - +
468D TYR* 3.6 12.0 + - + -
471D ARG* 2.8 24.2 + - - -
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Residues in contact with HIS 138 (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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72D VAL 3.1 21.1 + - - -
105D ILE* 3.2 24.1 - - + +
106D ASP 2.8 24.5 + - - +
107D HIS* 3.4 30.0 - + - +
108D VAL* 2.8 33.8 + - - +
137D LEU* 1.3 75.0 - - - +
139D VAL* 1.3 57.1 + - - +
140D ASP* 4.4 0.7 - - - +
163D SER* 2.6 30.8 + - - +
196D GLN* 3.0 25.2 + - - +
392D PHE* 3.4 31.4 - + - -
471D ARG* 4.1 0.9 - - - -
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Residues in contact with VAL 139 (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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108D VAL* 4.1 14.4 - - + -
110D PRO* 5.2 1.1 - - + -
116D LEU* 4.2 23.1 - - + +
120D PHE* 4.1 23.6 - - + -
137D LEU 4.6 0.4 - - - +
138D HIS* 1.3 76.9 - - - +
140D ASP* 1.3 73.2 + - - +
141D ILE* 4.1 0.2 - - - +
155D LEU* 4.2 12.3 - - + -
161D VAL* 3.8 23.6 - - + -
163D SER 3.1 6.6 + - - +
164D PHE* 3.0 44.2 - - + +
165D LEU 3.0 1.5 + - - -
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Residues in contact with ASP 140 (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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75D ARG* 3.0 34.4 + - - -
107D HIS* 2.9 27.5 + - - +
108D VAL 3.0 15.3 + - - +
109D VAL* 3.5 14.9 - - + +
110D PRO* 2.8 29.5 - - - +
116D LEU* 4.6 0.2 - - - +
138D HIS* 4.4 0.3 - - - +
139D VAL* 1.3 81.2 + - - +
141D ILE* 1.3 58.5 + - - +
165D LEU* 3.4 28.3 - - + +
167D TYR* 3.8 11.5 + - + -
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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