Contacts of the strand formed by residues 267 - 272 (chain A) in PDB entry 2RJF
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 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASN* 3.4 9.4 + - - -
263A VAL* 3.5 1.6 - - - -
264A CYS 2.9 31.8 + - - +
266A TYR* 1.3 80.7 - - - +
268A LEU* 1.3 64.5 + - - +
282A TRP* 3.2 43.2 + - + +
283A VAL 3.3 8.1 + - - +
284A ASN* 3.3 26.3 - - - +
458A VAL* 3.6 26.9 - - - +
463A PRO* 2.9 29.3 + - - +
464A ALA* 3.6 11.5 + - - +
466A ILE* 3.6 17.1 - - - +
500A ASP* 4.6 5.9 + - - -
502A HIS* 5.6 0.2 - - - -
506A TRP* 3.8 8.7 - - + -
512A HIS* 3.4 33.3 + - + -
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Residues in contact with LEU 268 (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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236A ASN* 4.2 3.1 - - - +
238A PHE* 4.0 31.2 - - + -
244A LEU* 5.4 0.4 - - + -
260A VAL* 4.1 11.7 - - + -
262A GLU 3.3 11.9 - - - +
263A VAL* 4.3 9.0 - - + -
267A ARG* 1.3 78.3 - - - +
269A ARG* 1.3 61.1 + - - +
270A LEU* 3.9 25.6 - - + -
281A PHE 3.9 0.3 - - - +
282A TRP* 3.3 9.3 - - - -
283A VAL* 2.9 47.0 + - + +
284A ASN 3.9 2.2 - - - +
285A ALA* 3.7 37.7 - - + +
290A ILE* 4.6 4.0 - - + -
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Residues in contact with ARG 269 (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 VAL* 3.6 5.5 - - - +
261A ALA* 2.8 51.2 + - + +
262A GLU* 2.8 52.6 + - + +
268A LEU* 1.3 74.3 - - - +
270A LEU* 1.3 59.4 + - - +
277A GLU* 5.6 2.4 - - - +
280A ASP* 2.8 47.3 + - + +
281A PHE 3.4 9.9 - - - +
282A TRP* 3.6 31.5 - - + +
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Residues in contact with LEU 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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244A LEU* 4.2 14.8 - - + -
258A LEU* 4.0 11.4 - - + -
259A THR 3.4 19.3 - - - +
260A VAL* 4.1 6.7 - - + -
261A ALA* 4.8 0.2 - - - -
268A LEU* 3.9 21.8 - - + -
269A ARG* 1.3 77.7 - - - +
271A HIS* 1.3 59.7 + - - +
272A PHE 4.3 0.2 + - - -
280A ASP* 3.2 9.1 - - - +
281A PHE* 2.7 64.3 + - + +
283A VAL* 3.6 28.7 - - + -
290A ILE* 3.9 19.5 - - + -
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Residues in contact with HIS 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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258A LEU* 3.2 8.4 - - - -
259A THR* 2.8 43.3 + - - +
261A ALA* 4.2 10.8 - - + -
270A LEU* 1.3 73.5 - - - +
272A PHE* 1.3 77.8 + - - +
273A ASP* 3.4 12.5 + - - +
274A GLY 4.6 2.4 + - - -
275A TYR 3.2 24.5 + - - -
276A SER 4.0 1.3 - - - -
277A GLU* 3.8 19.5 - - + +
280A ASP* 2.8 32.8 + - - +
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Residues in contact with PHE 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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247A ILE 5.2 0.4 - - - -
248A ASP* 3.6 32.3 - - + -
249A PRO* 4.2 0.7 - - + -
256A PHE* 3.6 44.9 - + + -
257A ILE 3.8 4.7 - - - +
258A LEU* 3.6 17.0 - - + -
271A HIS* 1.3 84.7 + - - +
273A ASP* 1.3 64.8 + - - +
275A TYR* 3.1 35.6 + + + +
276A SER 5.5 0.6 + - - +
279A HIS* 3.4 42.2 - - + -
280A ASP* 4.3 0.6 + - - -
281A PHE* 3.6 25.6 - + - -
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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