Contacts of the strand formed by residues 97 - 105 (chain A) in PDB entry 1VAV
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 ARG 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PRO* 4.4 10.7 - - - +
95A THR* 3.3 30.4 - - + +
96A ARG* 1.3 80.5 - - - +
98A MET* 1.3 68.3 + - - +
120A LEU* 3.2 44.2 - - + +
121A TYR 3.1 10.8 - - - +
122A GLN* 3.9 24.1 + - + +
129A ARG* 5.2 0.8 - - - +
131A GLN* 3.7 17.6 - - - +
133A LEU* 5.0 7.1 - - - +
201A GLN* 4.1 27.9 + - + +
202A ASP* 5.3 0.5 + - - +
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Residues in contact with MET 98 (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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89A ILE* 3.6 30.1 - - + -
91A ALA 3.5 20.0 - - - +
92A VAL* 4.1 6.3 - - + -
93A PRO* 4.1 6.5 - - - -
97A ARG* 1.3 78.2 - - - +
99A ILE* 1.3 65.9 + - - +
100A ILE* 3.6 4.5 + - + +
120A LEU* 3.6 4.8 - - - +
121A TYR* 2.9 35.9 + - + +
198A LEU* 3.5 30.5 - - + -
199A TYR 3.7 6.5 - - - +
200A LEU* 3.8 22.4 - - + +
201A GLN* 4.9 3.8 - - - -
211A GLY* 3.7 23.1 - - - -
212A ARG 4.1 4.5 - - - +
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Residues in contact with ILE 99 (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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61A GLU* 4.5 1.6 - - - +
98A MET* 1.3 70.8 - - - +
100A ILE* 1.3 61.8 + - - +
101A GLY 3.6 9.4 - - - +
102A GLN* 3.5 38.8 - - + +
118A LYS* 3.8 31.6 - - + -
119A LEU 3.3 6.7 - - - +
120A LEU* 3.5 27.8 - - + -
197A GLY 3.5 5.4 - - - +
198A LEU* 3.5 2.1 - - - -
199A TYR* 2.9 51.9 + - + +
201A GLN* 4.2 19.5 - - + +
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Residues in contact with ILE 100 (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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61A GLU* 5.7 0.7 - - - -
87A LEU* 4.3 8.5 - - + -
89A ILE* 4.2 11.0 - - + -
98A MET* 3.8 11.4 - - + +
99A ILE* 1.3 76.7 - - - +
101A GLY* 1.3 59.1 + - - +
119A LEU* 2.9 25.5 + - + +
121A TYR* 4.1 16.2 - - + +
130A VAL* 4.4 17.3 - - + -
158A PHE* 3.6 34.5 - - + -
160A TYR* 2.8 29.8 + - + -
197A GLY 3.3 22.3 + - - +
198A LEU* 4.1 17.7 - - + -
215A PHE* 3.6 7.6 - - - -
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Residues in contact with GLY 101 (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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61A GLU* 5.4 0.8 + - - -
99A ILE* 3.6 3.8 - - - +
100A ILE* 1.3 82.2 - - - +
102A GLN* 1.3 69.8 + - - +
119A LEU* 2.8 27.1 + - - -
160A TYR* 3.4 16.8 - - - -
162A ILE* 4.2 7.0 - - - -
195A LYS 3.4 9.9 - - - -
196A ALA* 4.4 0.2 - - - -
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Residues in contact with GLN 102 (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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59A ARG* 4.7 0.4 - - - +
61A GLU* 2.7 34.6 + - - +
83A LEU* 4.6 1.0 - - - +
99A ILE* 3.5 17.7 - - + +
101A GLY* 1.3 79.5 - - - +
103A ILE* 1.3 67.7 + - - +
104A HIS* 3.6 20.0 + - + +
115A PRO* 3.6 12.5 - - - +
117A VAL 3.1 13.5 - - - +
118A LYS* 3.6 9.2 - - + +
162A ILE* 4.1 8.6 - - - +
194A PHE* 3.5 8.5 - - - -
195A LYS* 2.9 49.4 + - + +
199A TYR* 3.9 17.9 - - - -
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Residues in contact with ILE 103 (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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74A TRP* 4.7 8.5 - - + -
102A GLN* 1.3 71.7 - - - +
104A HIS* 1.3 55.9 + - - +
115A PRO* 3.5 1.0 - - - +
116A LEU* 2.7 55.4 + - + -
117A VAL* 3.0 13.4 + - + +
162A ILE* 3.3 32.1 - - + -
163A GLY* 4.2 12.3 - - - +
164A VAL* 5.1 2.0 - - + -
170A LEU* 4.3 16.2 - - + -
192A LEU* 4.3 22.4 - - + -
193A TYR 3.4 8.7 - - - +
194A PHE* 3.4 30.3 - - + -
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Residues in contact with HIS 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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102A GLN* 3.6 21.7 + - + +
103A ILE* 1.3 76.5 - - - +
105A SER* 1.3 90.2 + - - +
113A ALA* 3.4 21.5 + - - +
114A ALA* 3.7 4.8 - - - -
115A PRO* 3.8 24.0 - - + +
116A LEU 4.7 0.7 - - - -
192A LEU* 3.4 7.5 - - - +
193A TYR* 2.7 69.0 + - + +
195A LYS* 4.4 12.3 - - + +
199A TYR* 6.6 0.2 - + - -
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Residues in contact with SER 105 (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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104A HIS* 1.3 93.1 - - - +
106A ASP* 1.3 64.2 + - - +
107A GLY* 3.2 13.4 + - - -
110A SER* 4.6 1.4 + - - -
112A GLN 4.6 2.0 + - - -
113A ALA* 3.6 7.4 - - - +
114A ALA 2.9 28.4 + - - -
138A PRO* 5.3 1.9 - - - +
187A TRP* 3.9 22.4 - - - -
190A GLN* 4.0 15.4 + - - +
191A GLY 3.4 8.1 + - - -
192A LEU* 4.1 2.0 - - - -
193A TYR* 3.5 4.0 + - - -
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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