Contacts of the strand formed by residues 270 - 275 (chain A) in PDB entry 3I7O
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 ARG 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ARG* 3.9 3.8 - - - +
264A VAL* 3.1 41.0 + - + +
265A ASP* 2.6 43.1 + - - +
268A GLY* 3.9 0.7 - - - -
269A SER* 1.3 87.4 + - - +
271A TYR* 1.3 71.3 + - - +
282A MET* 3.9 24.7 - - - +
283A LEU 3.7 1.8 - - - -
284A LEU* 3.8 30.7 - - + -
316A TYR* 4.9 7.9 + - - -
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ILE* 3.5 31.8 - - + +
221A ALA 3.6 10.4 + - - -
222A VAL* 3.7 6.5 - - + -
223A PRO* 3.3 16.3 - - - +
230A ILE* 4.3 21.3 - - + -
261A HIS* 5.0 1.6 - - + -
262A ASN 3.4 12.3 - - - -
263A ARG* 3.3 48.5 + - + -
264A VAL* 4.3 1.6 - - - +
268A GLY* 3.5 26.9 - - - -
270A ARG* 1.3 80.4 - - - +
272A LEU* 1.3 61.1 + - - +
273A LEU* 4.7 2.9 - - + -
282A MET* 3.3 10.3 - - - +
283A LEU* 2.6 60.0 + - + +
285A LEU* 5.1 1.1 - - + -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A HIS* 2.9 6.6 - - - -
262A ASN* 2.7 59.1 + - + +
264A VAL* 3.6 15.5 - - + +
271A TYR* 1.3 71.1 - - - +
273A LEU* 1.3 64.4 + - - +
280A LEU* 4.3 13.2 - - + -
281A PHE 3.6 13.9 - - - +
282A MET* 3.9 24.2 - - + -
305A LEU* 4.0 10.5 - - + -
314A LEU* 4.9 7.6 - - + -
315A THR 4.9 0.2 - - - -
316A TYR* 4.2 1.8 - - + +
322A VAL* 3.5 39.5 - - + -
336A LEU* 4.3 6.1 - - + -
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Residues in contact with LEU 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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220A ILE* 4.7 0.9 - - + -
232A ILE* 3.8 17.0 - - + -
237A ILE* 4.1 11.7 - - + -
258A ILE* 3.5 34.5 - - + -
260A CYS 3.2 3.1 - - - +
261A HIS* 3.6 21.1 - - + -
271A TYR* 4.7 3.6 - - + -
272A LEU* 1.3 85.7 - - - +
274A GLY* 1.3 59.8 + - - +
279A ARG 3.8 0.5 - - - +
280A LEU* 3.6 5.9 - - - +
281A PHE* 2.8 46.8 + - + +
283A LEU* 3.7 39.3 - - + -
302A VAL* 5.1 3.1 - - + -
314A LEU* 4.2 4.0 - - - -
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Residues in contact with GLY 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 3.1 9.9 - - - +
259A VAL* 2.7 29.9 + - - -
260A CYS* 2.7 30.2 + - - -
273A LEU* 1.3 73.5 - - - +
275A ASP* 1.3 57.3 + - - -
279A ARG 3.7 7.6 - - - -
280A LEU* 4.9 0.7 - - - -
281A PHE* 5.3 0.7 - - - -
311A ALA* 4.9 3.4 - - - -
314A LEU* 3.8 10.3 - - - +
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Residues in contact with ASP 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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256A SER* 2.5 39.3 - - - +
257A THR 2.9 15.0 - - - +
258A ILE* 5.0 0.9 - - - -
259A VAL* 4.2 10.0 - - - +
274A GLY* 1.3 73.5 - - - -
276A MET* 1.3 59.8 + - - +
277A GLU* 2.8 13.3 + - - +
278A GLY* 3.2 8.6 + - - +
279A ARG* 3.4 43.3 + - - +
281A PHE* 3.3 24.9 - - + -
310A ILE* 3.8 9.5 - - - +
311A ALA* 4.6 4.4 + - - +
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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