Contacts of the strand formed by residues 314 - 318 (chain B) in PDB entry 2DW1
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 THR 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B LEU* 3.8 4.2 - - - +
270B PHE* 3.9 23.6 - - + -
271B GLY* 3.9 4.5 - - - -
274B ARG* 4.0 26.0 - - + -
286B ASN* 4.0 0.8 - - - +
287B ALA* 3.2 16.6 - - + +
288B GLN* 4.0 0.2 - - - -
302B ALA* 3.9 3.5 - - - +
303B TYR* 3.7 18.0 + - - -
311B LYS 2.8 22.9 + - - +
312B ARG 2.8 5.6 + - - +
313B SER* 1.3 81.3 - - - +
315B GLY* 1.3 60.4 + - - +
338B ASN* 2.9 28.1 + - - -
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.6 6.9 - - - +
270B PHE* 3.9 2.8 - - - -
287B ALA 3.4 3.8 + - - -
288B GLN* 3.0 24.2 + - - +
289B LEU 3.0 17.0 + - - -
301B LEU 3.2 13.2 - - - -
302B ALA* 3.9 5.2 - - - -
314B THR* 1.3 79.5 - - - +
316B ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 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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263B ALA* 3.7 34.5 - - + +
266B THR* 4.0 21.8 - - + +
267B LEU* 3.9 23.3 - - + +
270B PHE* 4.6 3.4 - - + -
289B LEU* 3.5 21.5 - - + +
291B THR* 5.7 3.4 - - + -
295B LEU* 3.9 25.6 - - + -
300B GLY* 3.2 4.5 - - - -
301B LEU* 2.8 44.2 + - + +
315B GLY* 1.3 78.1 - - - +
317B ILE* 1.3 69.3 + - - +
334B GLU* 3.6 3.1 - - - +
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Residues in contact with ILE 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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288B GLN* 4.0 25.1 - - + +
289B LEU 2.8 14.4 + - - +
290B LEU* 3.4 15.5 - - + +
291B THR* 2.9 29.3 + - - +
295B LEU* 4.9 1.3 - - - -
299B ILE 3.7 3.4 - - - -
316B ILE* 1.3 82.4 - - - +
318B GLN* 1.3 71.3 + - - +
327B VAL* 4.5 8.7 - - + -
330B ILE* 3.4 27.6 - - + -
331B MET* 3.4 50.3 - - + +
334B GLU* 4.1 7.2 - - + -
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Residues in contact with GLN 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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290B LEU* 5.6 0.4 - - - -
291B THR* 3.3 6.7 - - - +
292B ALA 5.0 4.2 + - - -
293B ILE 3.6 19.7 - - - +
294B ASP* 3.2 25.4 + - - +
295B LEU* 2.9 27.4 + - + +
298B VAL 3.6 13.3 - - - +
299B ILE* 2.8 31.9 + - + +
317B ILE* 1.3 85.1 - - - +
319B ASP* 1.3 58.8 + - - +
320B TYR* 2.5 43.4 + - - +
327B VAL* 5.0 3.5 - - - +
330B ILE* 4.8 3.3 - - - +
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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