Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 1VRR
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 LEU 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 3.7 1.0 - - - -
9A HIS* 2.9 47.6 + - + +
12A GLY* 3.5 3.7 - - - -
141A LEU* 3.3 36.6 - - + -
145A HIS* 4.0 14.4 - - + -
156A VAL* 4.2 0.7 - - - -
157A GLY* 3.1 25.4 - - - +
159A GLU* 6.4 0.4 - - + -
184A VAL* 5.6 1.6 - - + -
192A PRO* 4.2 11.9 - - + -
194A VAL* 3.3 33.6 + - + +
195A PRO* 1.3 88.6 - - - +
197A VAL* 1.3 71.4 + - - +
198A LEU* 4.1 10.1 - - + -
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Residues in contact with VAL 197 (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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6A VAL* 4.2 11.9 - - + -
7A TYR 3.4 8.7 - - - +
12A GLY 3.4 8.1 - - - +
13A LEU* 3.3 42.4 - - + +
16A ILE* 4.3 9.0 - - + -
24A TRP* 4.7 2.9 - - + -
156A VAL* 3.9 9.0 - - + -
157A GLY 2.9 9.8 + - - +
158A VAL* 3.4 12.1 - - + +
159A GLU 3.0 24.2 + - - +
196A LEU* 1.3 80.6 - - - +
198A LEU* 1.3 61.1 + - - +
199A ILE* 3.7 23.6 + - + -
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Residues in contact with LEU 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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6A VAL* 3.4 3.1 - - - +
7A TYR* 2.8 65.6 + - + +
9A HIS* 6.0 0.2 - - + -
137A VAL* 6.0 0.2 - - + -
141A LEU* 4.1 23.6 - - + -
159A GLU* 3.4 26.9 - - + +
161A LEU* 5.1 10.1 - - + -
177A TYR* 3.7 14.9 - - + -
180A GLU* 5.0 0.9 - - + +
181A LEU* 4.3 25.6 - - + +
184A VAL* 4.4 16.2 - - + -
196A LEU* 4.5 11.0 - - + -
197A VAL* 1.3 72.9 - - - +
199A ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 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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3A ILE* 3.7 26.5 - - + -
5A GLU 3.5 2.7 - - - +
6A VAL* 4.3 6.3 - - + -
24A TRP* 3.8 27.4 - - + -
27A ILE* 4.1 13.2 - - + -
31A ILE* 4.1 9.6 - - + -
158A VAL* 4.0 20.6 - - + -
159A GLU 2.9 10.9 + - - +
160A ILE* 3.4 8.2 - - + -
161A LEU* 2.8 28.2 + - - +
177A TYR* 3.9 2.2 - - - -
197A VAL* 3.9 15.9 - - + +
198A LEU* 1.3 79.6 - - - +
200A GLY* 1.3 61.8 + - - +
201A ILE* 3.8 19.4 + - + -
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Residues in contact with GLY 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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4A VAL* 3.4 2.6 - - - +
5A GLU 2.7 28.1 + - - -
161A LEU 3.1 8.7 - - - -
163A MET* 2.9 25.9 - - - +
177A TYR* 3.4 24.6 - - - -
199A ILE* 1.3 71.8 - - - +
201A ILE* 1.3 62.6 + - - -
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Residues in contact with ILE 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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1A MET* 3.8 24.5 - - + -
2A ARG 3.4 13.0 - - - +
3A ILE* 4.7 1.3 - - - -
4A VAL 4.3 0.9 - - - +
31A ILE* 3.6 26.7 - - + -
64A PHE* 3.8 28.5 - - + -
131A PHE* 4.2 11.7 - - + -
160A ILE* 3.8 22.4 - - + -
161A LEU 3.0 12.5 + - - +
162A PRO* 3.3 6.0 - - + +
163A MET 2.9 17.8 + - - -
166A LEU* 4.5 1.1 - - + -
199A ILE* 4.0 15.7 - - + -
200A GLY* 1.3 69.9 - - - -
202A ALA* 1.3 69.5 + - - +
203A PRO* 4.6 2.0 - - + -
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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