Contacts of the strand formed by residues 258 - 264 (chain A) in PDB entry 2P2M
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 PRO 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A LYS* 6.3 0.2 - - - -
132A GLY* 6.1 3.1 - - - -
156A GLY* 4.6 9.4 - - - +
157A ALA 4.6 1.2 - - - +
158A VAL* 3.8 29.4 - - + +
256A GLU 3.5 4.7 - - - +
257A ASP* 1.3 93.4 - - + +
259A LEU* 1.3 59.8 + - - +
275A LEU* 4.3 26.2 - - + -
276A HIS 3.8 5.8 - - - +
277A THR* 4.1 6.3 - - + -
278A THR* 4.2 2.1 + - - -
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Residues in contact with LEU 259 (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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77A LEU* 3.7 27.6 - - + -
153A ALA* 3.7 34.0 - - + +
157A ALA 3.8 5.2 - - - +
158A VAL* 3.6 7.8 - - - -
159A HIS* 3.6 19.7 + - - +
257A ASP 3.5 0.2 + - - -
258A PRO* 1.3 73.5 - - - +
260A PHE* 1.3 81.4 + - + +
276A HIS 2.7 16.5 + - - +
277A THR 3.4 15.3 - - - +
278A THR* 3.9 13.2 - - + +
281A TYR* 3.6 28.3 - - + -
318A TYR* 4.5 4.9 - - + +
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Residues in contact with PHE 260 (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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158A VAL* 3.8 3.8 - - - +
159A HIS* 3.2 36.1 - + + +
259A LEU* 1.3 100.8 - - + +
261A ILE* 1.3 77.5 + - - +
262A LEU* 4.2 17.3 - - + -
275A LEU* 3.6 3.5 - - - +
276A HIS* 3.1 61.8 + + + +
281A TYR* 3.6 35.0 - + - -
310A VAL* 5.0 5.2 - - + -
313A HIS* 3.6 30.7 - + + -
318A TYR* 4.4 3.4 - + - -
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Residues in contact with ILE 261 (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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134A VAL* 5.1 5.2 - - + -
158A VAL* 3.7 18.2 - - + -
159A HIS 3.0 4.7 + - - +
160A SER* 3.4 33.5 + - - -
161A VAL 4.0 2.1 + - - -
178A SER* 5.8 1.6 - - - -
260A PHE* 1.3 82.9 - - - +
262A LEU* 1.3 64.1 + - - +
263A TYR* 4.1 14.4 - - + +
273A GLY* 3.3 35.9 - - - +
274A VAL 3.3 2.9 - - - -
275A LEU* 3.5 38.1 - - + -
313A HIS* 4.9 0.5 + - - -
478A PHE* 3.7 26.0 - - + -
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Residues in contact with LEU 262 (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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160A SER* 5.3 0.2 - - - -
161A VAL 3.4 24.7 - - - +
260A PHE* 4.2 5.4 - - + -
261A ILE* 1.3 74.6 - - - +
263A TYR* 1.3 65.7 + - - +
264A THR* 3.0 12.9 + - - +
273A GLY* 4.1 0.9 - - - -
274A VAL* 2.9 31.7 + - - +
308A GLY 3.5 17.7 - - - +
309A TRP* 3.9 2.9 - - + -
310A VAL* 3.4 45.8 - - + +
313A HIS* 3.7 30.1 - - + +
416A THR* 4.1 17.5 - - + +
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Residues in contact with TYR 263 (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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160A SER* 3.6 24.7 + - - -
161A VAL 5.3 2.1 + - - -
162A ILE* 5.9 0.4 - - + -
166A PHE* 5.8 0.7 - - - -
173A GLY 6.0 0.2 - - - -
174A ARG* 3.6 57.0 + - + +
177A ASP* 2.5 46.7 + - + +
178A SER* 3.3 19.2 + - - -
261A ILE* 4.1 10.0 - - + +
262A LEU* 1.3 80.3 - - - +
264A THR* 1.3 60.2 + - - +
271A PRO* 3.7 21.8 - - + -
272A LYS* 3.3 5.6 - - - -
273A GLY* 3.4 24.7 - - - -
309A TRP* 5.0 12.3 - - - -
478A PHE* 4.3 3.8 - - - -
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Residues in contact with THR 264 (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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262A LEU* 3.0 15.1 + - - +
263A TYR* 1.3 74.0 + - - +
265A SER* 1.3 62.4 + - - +
266A GLY* 3.7 0.9 + - - -
271A PRO* 3.2 6.5 - - - +
272A LYS* 2.9 27.4 + - - +
274A VAL* 3.4 13.3 - - - +
416A THR* 3.4 29.5 + - - +
417A GLU* 4.2 3.1 - - - +
488A TYR* 5.6 0.4 - - - +
526A ARG* 3.2 46.4 - - - +
998A PRX 4.5 0.4 - - - +
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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