Contacts of the strand formed by residues 317 - 322 (chain A) in PDB entry 2R9R
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 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG* 3.1 24.9 + - - -
217A TYR* 4.4 3.4 - - + -
225A VAL* 3.8 28.5 - - + -
240A ALA* 3.8 4.7 - - + +
242A THR* 4.0 22.7 - - + +
311A CYS 3.7 26.0 - - - +
312A LEU* 4.3 3.8 - - + -
314A ASN* 3.0 13.6 + - + +
315A GLU 3.5 5.5 - - - +
316A GLY* 1.3 79.5 - - - +
318A SER* 1.3 60.5 + - - +
319A SER 3.8 23.6 - - - +
320A VAL* 4.3 6.7 - - + -
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Residues in contact with SER 318 (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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40A ARG* 2.8 34.1 - - - +
41A ASN 3.0 14.5 + - - -
42A LEU* 3.6 21.0 - - - +
43A GLY* 2.9 26.9 + - - -
49A VAL* 4.1 2.7 - - - +
51A CYS* 3.8 4.2 - - - -
233A PHE* 5.4 2.1 - - - -
239A GLY* 4.3 4.2 - - - -
240A ALA 2.8 15.6 + - - -
312A LEU* 4.8 0.2 - - - -
315A GLU 5.0 2.8 + - - -
316A GLY 3.6 1.5 + - - -
317A VAL* 1.3 72.6 - - - +
319A SER* 1.3 64.9 + - - +
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Residues in contact with SER 319 (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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49A VAL* 4.0 7.6 - - - -
50A SER 2.8 24.1 + - - -
51A CYS 3.2 10.3 + - - -
52A LEU 3.6 1.2 + - - -
53A GLY 3.7 4.0 + - - -
83A LEU* 3.3 26.7 - - - +
240A ALA 3.6 1.2 + - - -
241A MET* 3.3 11.0 - - - +
242A THR* 3.0 25.8 + - - -
312A LEU* 4.5 1.8 - - - -
317A VAL* 3.5 3.7 - - - +
318A SER* 1.3 84.4 - - - +
320A VAL* 1.3 66.2 + - - +
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Residues in contact with VAL 320 (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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51A CYS 2.9 9.3 + - - +
52A LEU* 3.3 12.3 - - + +
53A GLY 2.8 22.7 + - - -
242A THR* 3.6 18.4 - - - +
245A PRO* 3.4 39.5 - - + -
308A ILE* 4.4 5.4 - - + +
311A CYS* 3.8 15.5 - - + -
312A LEU* 3.7 30.1 - - + -
317A VAL* 4.3 3.4 - - + -
319A SER* 1.3 77.0 + - - +
321A LEU* 1.3 64.7 + - - +
322A LEU* 3.6 8.2 + - + -
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Residues in contact with LEU 321 (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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53A GLY* 3.7 9.4 - - - -
54A LEU 4.7 1.8 - - - +
55A GLY 4.9 1.8 - - - +
83A LEU* 3.7 32.3 - - + -
85A ASP* 3.6 32.5 - - + +
214A GLN* 3.6 34.3 - - + +
241A MET* 3.9 12.6 - - + -
242A THR 2.9 19.9 + - - +
243A TRP* 4.7 1.6 - - + -
244A SER 4.2 0.7 + - - -
245A PRO* 3.2 22.8 - - - +
320A VAL* 1.3 71.6 - - - +
322A LEU* 1.3 60.1 + - - +
1001A NAP 3.3 30.0 - - - +
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Residues in contact with LEU 322 (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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52A LEU* 4.1 26.2 - - + -
53A GLY 2.9 19.8 + - - +
54A LEU* 3.7 8.1 - - + +
55A GLY* 2.8 27.4 + - - -
81A ILE* 5.1 2.0 - - + -
245A PRO* 4.1 12.3 - - + -
308A ILE* 3.5 44.4 - - + -
320A VAL* 4.3 6.1 - - + +
321A LEU* 1.3 74.2 - - - +
323A GLY* 1.3 63.5 + - - +
324A ALA* 5.9 0.2 - - + -
330A LEU* 4.2 19.3 - - + -
333A ASN* 4.0 23.1 - - + +
334A ILE* 4.8 2.0 - - + -
1001A NAP 3.7 4.1 - - - +
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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