Contacts of the strand formed by residues 195 - 201 (chain A) in PDB entry 3WOO
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 ASP 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A SER* 5.1 1.1 + - - -
193A ILE* 4.0 3.1 - - - +
194A LYS* 1.3 76.1 - - - +
196A VAL* 1.3 58.6 + - - +
197A ARG* 2.7 48.5 + - - +
229A ARG 3.9 0.7 - - - +
231A TYR* 3.0 39.6 + - + +
239A ALA 3.4 17.2 + - - +
241A PHE* 3.6 20.3 - - - +
242A SER 3.4 3.1 + - - -
245A ASN* 2.7 23.4 + - - +
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Residues in contact with VAL 196 (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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117A SER* 3.9 5.2 + - - -
118A ALA* 2.8 26.4 + - + +
119A GLY 4.4 2.6 + - - +
122A ALA* 3.8 16.3 + - + +
123A ARG* 3.7 37.5 - - - +
124A VAL* 3.8 14.8 - - + +
193A ILE* 4.1 9.4 - - + +
194A LYS 3.8 1.6 + - - -
195A ASP* 1.3 77.1 - - - +
197A ARG* 1.3 64.6 + - - +
228A TYR* 3.6 44.4 - - + -
229A ARG 3.7 5.8 - - - +
230A ALA* 5.5 0.2 - - - -
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Residues in contact with ARG 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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112A THR 5.1 2.8 + - - -
113A ALA* 6.1 0.2 - - - +
115A GLU* 3.9 26.1 + - + +
116A VAL 3.2 12.8 - - - +
117A SER* 4.3 3.1 - - - -
118A ALA* 3.9 0.9 - - - +
195A ASP* 2.7 39.1 + - - +
196A VAL* 1.3 80.7 - - - +
198A LEU* 1.3 60.0 + - - +
228A TYR* 3.0 11.1 - - - -
229A ARG 2.7 38.8 + - - +
231A TYR* 3.5 47.7 + - + -
241A PHE* 3.6 19.3 - - - -
242A SER 2.8 23.0 + - - -
243A LYS* 3.9 26.5 + - - +
245A ASN* 3.8 2.6 + - - +
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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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88A ALA* 4.6 5.4 - - + -
91A ALA* 4.8 4.7 - - + +
92A ILE* 4.0 39.9 - - + +
95A ASN* 5.0 1.1 - - - +
102A LEU* 4.8 4.9 - - + -
107A PHE* 3.3 47.0 - - + -
115A GLU* 3.4 17.3 - - - +
116A VAL* 2.8 27.7 + - + +
118A ALA* 4.2 9.9 - - - +
197A ARG* 1.3 70.7 - - - +
199A ALA* 1.3 57.9 + - - +
200A TYR 4.0 11.4 - - - +
201A ALA* 4.8 0.9 - - + -
227A PHE 3.6 16.4 - - - +
228A TYR* 4.2 17.3 - - + -
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Residues in contact with ALA 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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80A LEU* 4.4 10.5 - - + -
107A PHE* 4.0 3.1 - - - -
108A ASN* 4.4 1.4 - - - +
109A ALA* 3.1 28.0 + - + +
115A GLU* 3.8 27.6 - - + +
197A ARG 3.6 1.2 + - - -
198A LEU* 1.3 73.6 - - - +
200A TYR* 1.4 65.4 + - + +
227A PHE* 2.8 22.4 + - + +
228A TYR 4.3 10.1 - - - -
229A ARG 4.4 0.4 - - - +
714A LEU* 4.5 9.3 - - + +
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Residues in contact with TYR 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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107A PHE* 3.3 14.9 - - - -
108A ASN* 3.5 20.0 - - + -
198A LEU* 3.7 5.2 - - - +
199A ALA* 1.4 79.6 - - - +
201A ALA* 1.3 63.3 + - - +
202A PRO* 3.5 18.2 - - + +
225A PHE* 3.6 20.0 - + - -
226A ALA* 3.5 3.3 - - - +
227A PHE* 2.8 47.9 + + + +
704A ILE* 3.9 10.0 - - - +
705A MET* 3.7 14.1 - - + +
709A TYR* 2.7 55.2 + + - +
711A ALA* 3.5 19.3 - - + -
714A LEU* 3.6 17.0 - - + -
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Residues in contact with ALA 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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85A HIS* 4.5 0.7 - - + -
92A ILE* 3.6 36.3 - - + -
102A LEU 5.4 0.2 - - - +
106A GLY* 3.1 3.1 - - - -
107A PHE* 2.8 42.5 + - + +
198A LEU* 4.8 2.0 - - + -
200A TYR* 1.3 80.0 - - - +
202A PRO* 1.3 76.2 - - + +
226A ALA* 4.4 3.6 - - + -
709A TYR* 3.4 3.1 - - - -
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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