Contacts of the strand formed by residues 103 - 107 (chain A) in PDB entry 3VNG
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 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY 3.7 0.5 - - - +
99A VAL* 3.2 6.2 - - - -
100A ILE 3.0 33.4 + - - +
101A ASP* 2.9 27.5 + - + -
102A GLY* 1.3 84.2 + - - +
104A ILE* 1.3 63.3 + - - +
105A TYR* 3.9 7.0 + - + +
121A ARG* 3.6 28.5 - - + -
122A TYR 3.3 7.0 - - - +
123A GLU* 3.0 44.9 + - + +
124A PRO* 5.4 0.4 - - + -
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Residues in contact with ILE 104 (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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47A CYS* 3.8 24.7 - - - -
49A VAL* 3.9 17.9 - - + -
54A TYR* 3.6 42.4 - - + -
56A VAL* 4.6 9.0 - - + -
72A LEU* 4.5 4.7 - - + -
97A VAL* 4.4 8.7 - - + -
98A GLY 3.6 5.4 - - - +
99A VAL* 4.6 0.9 - - + +
103A HIS* 1.3 74.2 - - - +
105A TYR* 1.3 71.7 + - - +
106A ALA 3.9 0.3 + - - -
120A GLU 3.7 0.7 - - - +
121A ARG* 3.3 3.2 - - - -
122A TYR* 2.7 61.5 + - + +
124A PRO* 4.7 2.5 - - + -
129A TRP* 3.9 8.1 - - + -
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY 3.6 0.2 - - - +
97A VAL* 3.0 28.8 - - - +
98A GLY 2.7 22.4 + - - +
100A ILE* 3.8 34.7 + - + +
103A HIS* 3.9 12.1 - - + +
104A ILE* 1.3 77.6 - - - +
106A ALA* 1.3 60.2 + - - +
107A VAL* 3.8 2.7 + - + +
119A VAL* 4.4 13.5 - - + -
120A GLU 3.5 3.8 - - - -
121A ARG* 3.6 42.2 + - + -
132A VAL* 4.4 7.2 - - + -
151A LEU* 3.6 30.1 - - + -
169A TYR* 3.7 23.7 + + - -
171A PRO* 3.7 20.1 - - + +
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Residues in contact with ALA 106 (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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56A VAL* 4.6 1.3 - - + -
88A MET* 3.5 32.8 - - - -
92A ARG* 4.2 4.5 - - - -
95A ILE* 3.8 10.5 - - + -
96A GLY 3.6 4.0 - - - -
97A VAL* 4.3 2.0 - - - -
104A ILE 3.9 1.0 + - - -
105A TYR* 1.3 72.4 - - - +
107A VAL* 1.3 59.1 + - - +
108A GLY 4.3 0.2 + - - -
118A SER 4.4 0.2 - - - +
119A VAL* 3.2 8.1 - - - +
120A GLU* 2.8 33.8 + - + +
129A TRP* 3.6 17.3 - - + -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.7 1.9 - - - +
96A GLY 2.6 41.3 + - - +
105A TYR 4.1 5.8 - - - +
106A ALA* 1.3 79.0 - - - +
108A GLY* 1.3 70.6 + - - +
109A GLY 3.5 0.7 + - - -
119A VAL* 4.1 13.0 - - + -
135A MET* 3.3 31.4 - - + -
142A VAL* 3.6 6.7 - - + +
144A VAL* 3.9 25.6 - - + -
151A LEU* 3.8 29.4 - - + -
153A ALA* 4.3 6.1 - - + -
176A TRP* 4.6 1.3 - - + -
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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