Contacts of the strand formed by residues 134 - 139 (chain A) in PDB entry 3VJR
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 HIS 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.6 12.8 - - + +
90A ASP* 3.1 32.1 + - - +
92A ILE 2.8 16.1 + - - +
93A LEU* 3.8 15.7 - - + -
94A VAL 3.0 18.9 + - - -
109A LYS 3.3 8.0 + - - +
110A LEU* 4.0 37.0 - - + +
133A PHE* 1.3 78.7 - - - +
135A ARG* 1.3 65.0 + - - +
179A TRP* 3.5 27.6 - + + -
184A LEU* 4.3 14.9 - - + +
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.5 9.1 - - - +
94A VAL 3.2 11.9 - - - +
96A HIS* 3.8 21.2 + - + +
108A PHE* 3.4 8.0 - - - +
109A LYS* 2.6 54.6 + - + +
111A GLY 3.2 19.0 + - - -
112A GLY 2.9 19.4 + - - -
113A GLY 2.8 24.7 + - - -
120A LEU* 4.3 10.8 - - + +
124A ILE* 4.3 3.8 - - - +
131A PRO* 2.9 25.7 + - - +
133A PHE* 3.0 45.2 + - + -
134A HIS* 1.3 78.6 - - - +
136A LEU* 1.3 60.0 + - - +
137A ARG* 4.0 3.1 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.5 50.7 - - + -
93A LEU* 3.8 11.8 - - + +
94A VAL 2.9 6.5 + - - -
95A ALA* 4.0 11.0 - - + -
96A HIS* 3.0 30.2 + - - +
106A ALA* 4.0 9.4 - - + -
107A LYS 3.5 8.3 - - - +
108A PHE* 4.0 9.9 - - + -
135A ARG* 1.3 74.1 - - - +
137A ARG* 1.3 61.7 + - - +
138A ILE* 3.6 11.3 + - + +
172A ALA* 3.7 13.9 - - + -
176A THR* 4.8 1.8 - - - +
191A LEU* 3.9 25.8 - - + -
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 3.8 22.6 - - - +
98A GLU* 2.8 44.6 + - + +
100A ASP* 4.6 0.2 - - - +
101A LEU* 3.9 14.9 - - + +
106A ALA* 3.0 7.0 - - - -
107A LYS* 2.8 48.1 + - - +
108A PHE 5.6 0.4 + - - -
109A LYS* 3.9 37.6 - - + +
135A ARG* 4.5 7.2 - - + -
136A LEU* 1.3 70.5 - - - +
138A ILE* 1.3 62.6 + - - +
139A GLY 3.6 0.9 + - - -
3B G 3.2 36.3 + - - -
4B G 2.7 30.3 + - - -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 3.7 34.1 - - + +
27A GLY* 3.9 9.0 - - - +
30A PHE* 4.0 15.5 - - + -
95A ALA* 4.2 4.7 - - + -
96A HIS 2.8 27.1 + - - +
97A ASP* 3.4 3.8 - - - -
98A GLU* 2.7 27.5 + - - +
105A VAL 4.1 4.5 - - - +
106A ALA* 4.3 7.6 - - + -
136A LEU* 4.1 15.3 - - + -
137A ARG* 1.3 73.0 - - - +
139A GLY* 1.3 63.8 + - - +
140A ILE* 3.3 1.6 + - + +
165A ILE* 4.0 16.8 - - + +
168A ALA* 5.1 3.4 - - + -
169A ILE* 3.9 28.3 - - + -
172A ALA* 5.8 0.2 - - + -
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU 3.4 5.4 - - - -
101A LEU* 3.3 24.8 - - - +
102A PRO 3.4 13.9 - - - -
103A PRO* 3.5 13.9 - - - +
104A GLY 4.3 1.6 + - - -
105A VAL 2.9 16.7 + - - +
137A ARG 3.6 1.8 + - - -
138A ILE* 1.3 75.3 - - - +
140A ILE* 1.3 62.9 + - - +
165A ILE* 3.6 9.4 - - - +
168A ALA* 6.0 0.2 - - - +
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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