Contacts of the strand formed by residues 272 - 280 (chain H) in PDB entry 2W3S
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 272 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H LEU* 5.0 4.9 - - - -
167H GLU* 3.6 5.9 - - - +
168H ILE* 2.9 37.2 + - + +
270H HIS* 3.4 24.9 - - + -
271H ASP* 1.3 76.5 - - - +
273H ARG* 1.3 63.1 + - - +
274H ILE* 4.2 16.6 - - + -
293H HIS* 3.7 41.1 - + + -
294H LEU 2.9 14.8 - - - -
295H ALA* 3.7 20.0 - - + -
307H VAL* 5.4 1.1 - - + -
308H CYS* 4.3 13.9 - - + -
311H ALA* 3.8 20.9 - - + -
328H SER* 5.9 0.2 - - - -
345H GLY* 5.3 2.7 - - - -
348H GLN* 3.5 28.5 - - + -
349H GLY 5.5 0.2 - - - -
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Residues in contact with ARG 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H THR* 5.9 2.2 + - - -
129H LEU* 3.3 37.7 - - + +
130H ASP* 3.5 34.5 + - - +
165H CYS* 4.1 20.6 - - - -
166H PHE 3.3 9.4 - - - +
167H GLU* 2.8 33.7 + - - +
272H PHE* 1.3 73.5 - - - +
274H ILE* 1.3 68.1 + - - +
275H ARG* 4.2 9.9 - - - +
292H VAL 3.7 1.7 - - - +
294H LEU* 2.8 66.4 + - + +
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Residues in contact with ILE 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H CYS* 3.2 4.5 - - - -
166H PHE* 2.9 40.4 + - + +
168H ILE* 3.4 32.1 - - + +
272H PHE* 4.2 12.1 - - + -
273H ARG* 1.3 79.4 - - - +
275H ARG* 1.3 73.2 + - - +
276H TYR* 4.0 8.7 + - + +
291H PHE* 4.0 20.4 - - + -
292H VAL 3.4 4.3 - - - +
293H HIS* 3.6 24.0 - - + +
348H GLN 3.6 16.8 - - - +
352H GLY* 3.8 19.1 - - - -
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Residues in contact with ARG 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H LEU* 6.1 0.6 - - - +
164H GLY 3.5 11.0 - - - +
165H CYS* 4.1 14.5 - - + +
273H ARG* 4.2 12.3 - - - +
274H ILE* 1.3 77.2 - - - +
276H TYR* 1.3 67.1 + - - +
277H ARG* 6.0 3.6 - - + -
290H ASP 3.7 0.8 - - - +
291H PHE* 3.3 5.7 - - - -
292H VAL* 3.0 63.7 + - + +
294H LEU* 4.4 19.6 - - - +
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Residues in contact with TYR 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H ALA* 3.5 12.3 - - + -
163H GLU* 3.6 2.9 - - - +
164H GLY* 2.8 60.2 + - - +
165H CYS 3.8 3.1 - - - -
166H PHE* 4.1 10.5 - + - -
274H ILE* 4.3 8.1 - - + -
275H ARG* 1.3 79.1 - - - +
277H ARG* 1.3 69.1 + - - +
278H ILE* 4.7 1.1 - - + -
290H ASP 3.2 5.2 - - - +
291H PHE* 4.0 23.3 - - + -
352H GLY 4.6 4.7 - - - -
355H ARG* 3.2 33.9 + - - -
356H ALA* 3.9 26.5 - - + -
359H HIS* 2.6 44.6 - + + -
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Residues in contact with ARG 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H GLU* 3.2 27.9 + - - -
155H LEU* 3.9 46.8 - - + +
156H ALA* 5.6 1.2 - - - +
161H LEU* 4.9 6.8 - - + +
162H ALA 3.5 4.5 - - - -
163H GLU* 3.6 41.2 + - + +
275H ARG* 6.0 3.4 - - + -
276H TYR* 1.3 78.6 - - - +
278H ILE* 1.3 60.8 + - - +
289H ALA* 3.5 1.9 - - - -
290H ASP* 2.8 54.6 + - + -
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Residues in contact with ILE 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H LEU* 3.6 4.0 - - - -
161H LEU* 3.2 7.1 - - - +
162H ALA* 2.8 46.6 + - + +
276H TYR* 4.7 0.4 - - + -
277H ARG* 1.3 75.0 - - - +
279H GLY* 1.3 60.8 + - - +
286H LEU* 3.9 23.8 - - + -
288H GLY 3.6 11.2 - - - +
289H ALA* 4.4 8.7 - - + -
291H PHE* 5.2 0.2 - - + -
353H MET* 3.7 24.0 - - - -
356H ALA* 3.7 34.5 - - + +
357H ILE* 4.0 10.1 - - + +
360H LEU* 3.7 26.7 - - + -
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Residues in contact with GLY 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H LEU* 3.5 11.8 - - - +
158H ALA* 4.4 4.3 - - - -
160H HIS 3.2 13.7 - - - -
161H LEU* 4.2 0.4 - - - -
278H ILE* 1.3 78.4 - - - +
280H ALA* 1.3 55.0 + - - -
286H LEU* 3.7 1.4 - - - +
287H LEU* 2.6 39.4 + - - +
288H GLY 3.0 12.6 + - - +
360H LEU* 4.1 4.0 - - - -
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Residues in contact with ALA 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H ALA 3.5 1.6 + - - -
160H HIS* 3.1 28.6 + - + +
279H GLY* 1.3 73.6 - - - -
281H ASP* 1.3 64.8 + - - +
284H GLY* 3.8 16.4 - - - +
285H LYS 3.0 20.2 - - - +
286H LEU* 4.2 2.0 - - + +
287H LEU* 3.3 12.7 - - - +
360H LEU* 3.7 20.8 - - + +
364H MET* 4.2 11.2 - - + -
371H LEU* 5.3 0.2 - - + -
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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