Contacts of the strand formed by residues 314 - 318 (chain B) in PDB entry 2DOU
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 TYR 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLY* 4.0 16.6 - - - -
168B ASN 4.2 7.0 - - - -
169B ASN* 3.3 34.6 + - + -
170B PRO 3.5 18.8 - - - +
171B THR 4.8 0.7 - - - +
172B GLY* 4.4 6.3 - - - +
200B TYR* 3.6 24.4 + + - -
205B TYR* 4.7 1.4 + - - -
230B LYS* 3.9 13.0 + - - -
311B ALA 4.1 5.4 - - - +
312B THR* 3.0 29.8 + - - +
313B MET* 1.3 96.2 - - + +
315B LEU* 1.3 67.8 + - - +
354B ARG* 3.5 40.8 - - + -
355B ILE 3.2 4.7 - - - +
356B ALA* 4.3 5.4 - - + -
357B LEU* 4.6 3.2 - - - +
505B SO4 3.5 13.3 + - - -
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PRO 4.5 0.7 - - - -
171B THR 5.4 0.2 - - - -
293B ALA* 3.8 24.7 - - + +
296B MET* 4.3 18.8 - - + -
297B ALA* 4.5 5.4 - - + +
300B LEU* 4.7 7.0 - - + -
306B LEU* 4.2 20.4 - - + -
307B LEU 5.5 2.2 - - - +
309B PRO* 4.0 29.6 - - + -
314B TYR* 1.3 80.8 - - - +
316B TRP* 1.3 60.6 + - - +
317B GLY 4.1 0.7 - - - -
353B VAL 3.8 0.7 - - - +
354B ARG* 3.5 7.6 - - - +
355B ILE* 2.9 43.6 + - + +
357B LEU* 3.6 25.4 - - + -
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Residues in contact with TRP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 4.1 15.6 - - + +
140B LEU* 5.7 2.2 - - - +
144B GLY* 6.4 0.2 - - - -
170B PRO* 3.4 36.3 - - + +
171B THR* 3.6 47.3 + - + +
305B SER 4.0 0.5 - - - +
306B LEU* 3.2 11.5 - - - +
307B LEU* 2.9 43.0 - - + +
314B TYR 4.3 0.2 - - - -
315B LEU* 1.3 75.0 - - - +
317B GLY* 1.3 57.5 + - - +
318B ARG 4.4 0.2 + - - -
342B GLY* 3.5 35.9 - - - -
345B PHE* 4.0 3.1 - + - -
348B GLY 4.7 0.2 - - - -
349B GLY* 4.0 16.2 - - - -
352B PHE* 3.3 48.0 - + + -
353B VAL 3.6 14.1 - - - -
354B ARG* 4.0 7.9 - - + -
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B LEU* 4.3 14.3 - - - +
305B SER 3.7 2.2 - - - -
306B LEU* 3.4 17.8 - - - +
315B LEU 4.1 0.4 - - - -
316B TRP* 1.3 75.0 - - - +
318B ARG* 1.3 62.2 + - - -
319B LEU 3.6 0.7 + - - -
352B PHE* 3.2 8.6 - - - -
353B VAL* 3.1 40.2 + - - +
355B ILE* 6.1 0.6 - - - +
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B VAL 4.5 0.2 - - - +
304B LEU* 3.7 6.9 - - - -
305B SER* 3.1 47.8 + - - +
317B GLY* 1.3 70.8 - - - -
319B LEU* 1.3 74.1 + - - +
320B PRO* 3.9 0.3 - - - +
351B GLY 3.6 4.5 - - - +
352B PHE* 3.3 47.4 - - + -
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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