Contacts of the strand formed by residues 197 - 202 (chain A) in PDB entry 3VAG
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 PHE 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR* 3.7 30.7 - + + +
153A VAL 3.4 11.7 - - - +
154A GLY* 4.5 0.4 - - - -
156A ILE* 4.0 5.8 - - - +
191A ILE* 3.7 3.5 - - - +
192A ASN* 2.9 64.2 + - + +
195A LYS* 3.7 28.9 - - + +
196A ASN* 1.3 80.3 - - - +
198A ALA* 1.3 69.3 + - - +
199A PHE* 3.9 21.8 - + - -
405A SO4 4.2 12.3 - - - -
4P U 4.2 3.4 - - + -
5P U 3.7 30.7 - - - -
6P U 4.4 9.6 - - - -
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Residues in contact with ALA 198 (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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152A TYR* 3.7 0.7 - - - -
153A VAL* 2.9 38.2 + - + +
156A ILE* 4.5 3.6 - - + -
165A MET* 4.1 21.8 - - - -
189A VAL* 4.2 6.3 - - + -
190A GLN 3.2 12.6 - - - +
191A ILE* 4.0 15.9 - - + -
197A PHE* 1.3 77.3 - - - +
199A PHE* 1.3 71.9 + - - +
200A LEU* 5.3 0.7 - - + -
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Residues in contact with PHE 199 (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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150A ARG* 3.5 33.9 - - + +
151A LEU 3.3 18.2 - - - -
152A TYR* 4.0 17.9 - + + -
188A ALA 4.8 0.2 - - - -
189A VAL* 3.5 4.2 - - - +
190A GLN* 3.0 40.0 + - - +
197A PHE* 3.9 13.0 - + - -
198A ALA* 1.3 76.9 - - - +
200A LEU* 1.3 62.0 + - - +
201A GLU* 5.6 0.3 - - - +
229A PRO* 4.1 11.2 - - + -
405A SO4 4.3 5.6 - - - +
5P U 3.3 40.4 - + - -
6P U 3.4 49.4 - + - -
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Residues in contact with LEU 200 (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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149A ARG 3.9 0.2 - - - +
150A ARG* 3.2 10.1 - - - +
151A LEU* 3.1 34.0 + - + +
153A VAL* 3.8 22.7 - - + -
165A MET* 4.3 5.6 - - + -
169A PHE* 3.8 48.9 - - + -
186A VAL* 4.6 6.5 - - + -
188A ALA 3.7 3.1 - - - +
189A VAL* 3.7 32.1 - - + -
198A ALA* 5.3 0.7 - - + -
199A PHE* 1.3 75.1 - - - +
201A GLU* 1.3 59.7 + - - +
202A PHE* 3.7 30.4 - - + -
211A ALA* 5.9 0.2 - - + -
226A ILE* 5.5 0.4 - - + -
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Residues in contact with GLU 201 (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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149A ARG* 3.6 7.8 + - - +
150A ARG* 4.6 10.2 + - - +
186A VAL* 3.6 3.9 - - - -
187A LEU* 2.9 43.5 + - + +
188A ALA* 3.0 34.7 + - + +
190A GLN* 5.6 5.1 + - - -
199A PHE 5.6 0.2 - - - +
200A LEU* 1.3 72.7 - - - +
202A PHE* 1.3 68.7 + - - +
406A SO4 3.3 37.8 + - - +
7P U 5.6 0.5 - - - +
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Residues in contact with PHE 202 (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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149A ARG* 2.9 39.2 + - - +
151A LEU* 4.0 19.3 - - + -
169A PHE* 5.6 1.6 - + - -
173A MET* 4.6 9.0 - - + -
185A PRO* 3.3 20.4 - - + -
186A VAL* 3.8 17.3 - - + -
187A LEU* 4.1 4.8 - - - +
200A LEU* 3.7 38.8 - - + -
201A GLU* 1.3 78.9 - - - +
203A ARG* 1.3 63.8 + - - +
204A SER 3.3 5.8 - - - +
207A GLU* 4.0 14.6 - - + -
208A THR* 3.2 30.3 - - + +
211A ALA* 3.6 31.9 - - + -
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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