Contacts of the strand formed by residues 173 - 178 (chain A) in PDB entry 2WMN
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 GLU 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG* 3.6 32.0 + - - -
158A VAL 3.3 6.3 - - - +
159A ALA* 3.7 18.6 - - + +
161A PHE* 5.8 1.6 - - + -
171A GLY 3.5 7.5 + - - +
172A LYS* 1.3 74.3 - - - +
174A TYR* 1.3 63.0 + - - +
226A GLN* 4.8 1.9 - - - +
295A PRO* 3.6 5.9 - - - +
296A VAL* 2.9 40.2 + - + +
299A GLN* 2.5 33.0 + - - +
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Residues in contact with TYR 174 (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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156A PHE 3.5 0.3 - - - +
157A ARG* 3.3 6.2 - - - +
158A VAL 2.8 33.8 + - - -
160A PHE* 4.0 16.4 - + - -
169A GLU* 2.8 39.6 + - - -
172A LYS* 3.9 23.2 - - + +
173A GLU* 1.3 76.4 - - - +
175A ILE* 1.3 64.5 + - - +
176A TYR* 3.5 22.7 - + + -
293A ARG* 3.7 37.6 + - + -
294A ILE 3.4 6.5 - - - +
295A PRO* 3.7 36.2 - - + +
296A VAL* 4.2 3.1 - - - +
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Residues in contact with ILE 175 (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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155A TYR* 3.9 22.4 - - + -
156A PHE 3.2 9.4 - - - +
157A ARG* 4.4 8.3 - - - -
174A TYR* 1.3 76.0 - - - +
176A TYR* 1.3 63.0 + - - +
230A VAL* 4.6 3.8 - - + -
255A PHE* 4.0 29.8 - - + -
281A LEU* 4.4 18.6 - - + -
283A ALA* 4.3 12.6 - - + +
287A PHE* 3.5 29.3 - - + -
293A ARG* 3.1 5.0 - - - +
294A ILE 2.9 37.2 + - - +
296A VAL* 4.1 16.6 - - + -
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Residues in contact with TYR 176 (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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154A THR 3.8 0.7 - - - +
155A TYR* 3.2 7.1 - - - -
156A PHE* 2.7 37.1 + - + +
158A VAL* 3.5 38.4 - - + -
160A PHE* 3.3 15.0 - + - -
174A TYR* 3.5 25.8 - + + -
175A ILE* 1.3 75.2 - - - +
177A LYS* 1.3 59.5 + - - +
178A GLU* 3.8 20.8 + - + +
187A ILE* 4.3 11.7 - - + -
191A LEU* 4.3 20.0 - - + +
195A TYR* 4.8 2.8 + - - -
292A LYS* 3.7 13.7 - - - -
293A ARG* 3.0 44.0 + - + -
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Residues in contact with LYS 177 (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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26A ASP* 5.4 1.4 - - - +
28A SER* 4.3 10.1 + - - -
29A GLU* 2.8 34.7 + - - +
103A ARG* 3.8 14.1 - - - +
152A LEU 3.6 22.6 + - - +
153A GLY* 5.1 0.6 - - - -
154A THR 3.6 4.5 - - - +
155A TYR* 3.2 42.2 - - + +
175A ILE 4.1 0.2 + - - -
176A TYR* 1.3 71.6 - - - +
178A GLU* 1.3 68.5 + - - +
179A PRO* 4.7 0.7 - - - +
287A PHE* 3.8 18.1 - - + -
288A PRO* 4.9 5.2 - - + -
292A LYS* 2.9 41.8 + - - +
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Residues in contact with GLU 178 (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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153A GLY* 3.3 6.6 - - - -
154A THR* 2.7 34.1 + - - +
156A PHE* 3.8 23.1 - - + -
176A TYR* 3.8 13.1 - - - +
177A LYS* 1.3 78.3 + - - +
179A PRO* 1.3 76.4 - - + +
182A THR* 3.6 19.1 - - + -
187A ILE* 3.9 15.3 - - + -
190A ARG* 2.7 33.6 + - - -
292A LYS* 2.5 33.2 + - - -
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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