Contacts of the strand formed by residues 97 - 102 (chain A) in PDB entry 3R2W
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 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL 4.1 0.4 + - - +
94A LEU* 3.1 19.6 + - + +
95A ASN 3.6 0.8 - - - -
96A LYS* 1.3 79.2 - - - +
98A VAL* 1.3 66.9 + - - +
99A VAL* 3.9 22.0 - - + -
146A VAL* 3.7 19.6 - - + +
147A PRO* 3.8 0.9 - - - +
233A LYS* 3.7 10.2 + - - -
235A TYR* 3.2 21.8 - - + +
236A ILE 4.0 0.2 - - - -
237A PHE* 3.5 29.4 - - + +
248A VAL* 4.1 16.2 - - + -
253A LEU* 3.8 39.5 - - + -
322A TRP* 3.9 7.6 - - + -
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Residues in contact with VAL 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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97A LEU* 1.3 80.0 - - - +
99A VAL* 1.3 65.1 + - - +
100A VAL* 3.5 1.1 + - + -
147A PRO* 3.9 17.0 - - + +
149A VAL* 3.4 31.9 - - + -
228A PHE* 3.7 34.3 - - + -
233A LYS* 3.7 21.1 - - + -
235A TYR 2.7 11.5 + - - +
236A ILE* 3.4 21.3 - - + +
237A PHE 2.8 26.7 + - - -
325A LEU* 4.6 0.4 - - + -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.9 18.4 + - + -
98A VAL* 1.3 72.2 - - - +
100A VAL* 1.3 57.7 + - - +
101A LYS* 4.2 27.6 - - + -
131A THR* 6.3 1.1 - - - -
135A ILE* 4.2 21.1 - - + -
146A VAL* 4.2 7.0 - - + -
147A PRO 3.5 12.5 + - - +
148A LEU* 3.4 11.7 - - + +
149A VAL* 2.8 30.3 + - - +
237A PHE* 4.2 14.4 - - + +
248A VAL* 3.7 28.5 - - + -
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Residues in contact with VAL 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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98A VAL 3.5 1.0 + - - +
99A VAL* 1.3 76.1 - - - +
101A LYS* 1.3 73.6 + - - +
102A LEU* 5.4 0.4 - - + -
149A VAL* 3.3 31.0 - - + +
151A MET* 4.8 3.8 - - + -
177A PHE* 4.6 10.8 - - + -
215A ILE* 4.5 12.1 - - + -
219A PHE* 4.7 6.1 - - + -
236A ILE* 3.3 37.7 - - + -
237A PHE 2.9 20.3 + - - +
238A VAL* 4.0 20.6 - - + -
239A SER 3.2 12.3 + - - -
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Residues in contact with LYS 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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99A VAL* 4.1 19.0 + - + -
100A VAL* 1.3 82.4 - - - +
102A LEU* 1.3 61.1 + - - +
103A ASN* 3.6 1.6 + - + +
131A THR* 2.9 34.7 - - + +
134A GLN* 4.5 3.1 + - - +
148A LEU* 4.7 10.1 - - + -
149A VAL 2.9 7.5 + - - +
150A LEU* 3.4 10.9 - - + +
151A MET* 3.0 23.9 + - - +
237A PHE* 5.5 1.8 - - - -
239A SER* 3.0 24.8 + - - +
240A ASN 4.2 14.7 + - - +
241A ILE* 3.9 28.1 - - + +
243A ASN 4.3 6.7 + - - -
246A ALA 3.4 21.6 + - - -
248A VAL* 6.5 0.4 - - - -
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Residues in contact with LEU 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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100A VAL* 5.4 0.9 - - + -
101A LYS* 1.3 71.1 - - - +
103A ASN* 1.3 58.7 + - - +
104A GLY 3.6 3.5 + - - +
151A MET* 3.8 39.3 - - + +
212A HIS* 3.7 35.0 - - + +
215A ILE* 4.5 5.8 - - + -
238A VAL* 3.8 24.7 - - + -
239A SER 3.0 19.8 + - - +
240A ASN* 3.3 34.2 + - + +
241A ILE* 3.1 21.2 - - - +
319A ASN* 5.2 7.6 - - - +
361A VAL* 5.1 2.5 - - + -
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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