Contacts of the strand formed by residues 269 - 275 (chain A) in PDB entry 2CG2
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 VAL 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ILE* 4.2 11.0 - - + -
129A ARG 3.3 26.7 - - - +
130A GLY* 3.8 15.0 - - - -
131A ASP 4.9 0.4 - - - +
135A ILE* 4.4 2.2 - - + -
265A VAL* 3.8 2.0 - - - -
266A LEU 2.7 41.1 + - - +
267A ASP 4.1 0.2 - - - +
268A GLY* 1.3 72.3 - - - +
270A PRO* 1.3 76.9 - - + +
271A PHE* 3.1 26.5 - - + -
289A LEU* 4.3 5.4 - - + -
291A ARG* 3.5 25.6 - - - +
292A GLN* 4.8 5.4 - - - +
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Residues in contact with PRO 270 (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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264A LEU 3.6 5.8 - - - +
265A VAL* 4.2 11.8 - - + -
268A GLY 3.8 7.2 - - - +
269A VAL* 1.3 88.7 - - + +
271A PHE* 1.3 59.0 + - - +
289A LEU* 3.6 13.3 - - - +
290A PRO* 3.4 36.3 - - + +
291A ARG* 4.2 27.1 - - + +
292A GLN* 5.6 0.2 - - - +
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Residues in contact with PHE 271 (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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128A ILE* 3.8 25.8 - - + -
135A ILE* 3.6 22.4 - - + -
137A VAL* 4.8 0.2 - - + -
166A ILE* 3.6 18.6 - - + -
263A ASP* 3.3 4.5 - - - +
264A LEU 2.7 39.0 + - - +
266A LEU* 3.9 19.5 - - + -
269A VAL* 3.1 45.8 - - + -
270A PRO* 1.3 75.8 - - - +
272A THR* 1.3 62.8 + - - +
273A PHE* 3.7 35.2 - + + -
287A ILE* 3.7 18.6 - - + -
288A TRP 3.7 3.8 - - - -
289A LEU* 3.7 12.1 - - + -
290A PRO* 5.0 0.9 - - - -
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Residues in contact with THR 272 (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 GLU 3.5 3.8 - - - +
263A ASP* 2.7 26.3 + - - +
271A PHE* 1.3 73.0 - - - +
273A PHE* 1.3 71.7 + - - +
274A GLN* 4.1 0.3 + - - +
286A ASN 3.8 0.2 - - - +
287A ILE* 3.3 5.0 - - - +
288A TRP* 2.8 57.6 + - - +
290A PRO* 4.8 4.4 - - - +
332A ARG* 3.6 25.6 - - - +
333A PHE* 4.0 14.1 - - + -
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Residues in contact with PHE 273 (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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166A ILE* 3.8 23.3 - - + -
195A ILE* 4.5 6.3 - - + -
257A ILE* 3.7 34.5 - - + -
261A GLY* 3.1 5.1 - - - -
262A GLU 2.8 36.2 + - - +
264A LEU* 3.8 25.4 - - + -
266A LEU* 4.2 5.6 - - + -
271A PHE* 3.7 34.8 - + + -
272A THR* 1.3 80.8 - - - +
274A GLN* 1.3 59.8 + - - +
275A ASN 4.0 0.7 - - - -
285A MET* 3.7 28.5 - - + -
286A ASN 3.4 1.8 - - - -
287A ILE* 3.7 28.0 - - + -
332A ARG* 4.9 1.9 + - - -
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Residues in contact with GLN 274 (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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260A GLU 3.7 5.4 - - - +
272A THR 4.1 0.4 + - - -
273A PHE* 1.3 71.6 - - - +
275A ASN* 1.3 69.1 + - - +
276A THR* 3.4 3.3 + - - +
285A MET* 3.8 2.5 - - - -
286A ASN* 2.7 69.6 + - + +
325A TYR* 3.5 31.7 + - + -
328A GLN* 3.6 17.2 - - - +
329A ALA* 3.4 22.4 - - - +
332A ARG* 4.4 16.0 - - - +
333A PHE* 3.6 24.0 - - + -
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Residues in contact with ASN 275 (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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197A PRO* 3.2 36.0 - - - +
198A ALA* 4.8 3.4 - - - +
257A ILE* 2.9 31.2 + - - +
258A GLU 3.8 1.2 - - - +
259A GLY 3.0 28.9 + - - +
260A GLU* 3.0 14.3 + - - +
261A GLY 4.1 0.3 + - - -
273A PHE 4.0 1.0 - - - -
274A GLN* 1.3 78.4 - - - +
276A THR* 1.3 59.6 + - - +
277A PRO* 3.5 12.7 - - + +
284A GLU 3.5 2.9 + - - +
285A MET* 3.5 11.9 - - - +
325A TYR* 3.4 18.2 - - - -
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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