Contacts of the strand formed by residues 307 - 318 (chain B) in PDB entry 2W77
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 307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B PRO* 3.6 4.2 - - - +
301B LEU* 2.7 50.3 + - + -
302B THR* 3.5 26.0 + - + -
305B GLY 3.9 2.1 - - - +
306B ASN* 1.3 94.3 + - - +
308B ARG* 1.3 62.2 + - - +
336B LEU* 5.4 1.6 - - + -
337B GLU 3.4 4.9 - - - +
338B PHE* 3.8 41.1 - - + -
339B ASP 5.2 0.2 - - - +
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Residues in contact with ARG 308 (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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273B PRO* 3.8 13.9 - - + -
274B THR* 3.8 21.3 - - - +
275B HIS* 3.4 45.9 + - - +
299B GLY 3.6 7.4 - - - +
300B PRO* 4.3 4.7 - - + -
301B LEU* 4.2 6.3 - - - +
305B GLY 3.0 23.1 + - - +
306B ASN 4.3 0.4 + - - -
307B VAL* 1.3 76.4 - - - +
309B GLY* 1.3 56.8 + - - +
336B LEU* 3.2 6.9 - - - +
337B GLU* 2.7 85.8 + - + +
339B ASP* 2.6 39.7 + - - -
345B MET* 4.0 9.5 - - - -
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PRO* 3.6 6.6 - - - +
297B VAL 4.0 0.2 - - - +
298B SER* 3.4 3.8 + - - -
299B GLY 3.0 33.3 + - - +
301B LEU* 4.2 16.2 - - - +
308B ARG* 1.3 76.5 - - - +
310B ARG* 1.3 60.3 + - - -
335B ILE 3.0 11.4 - - - -
336B LEU* 4.4 1.8 - - - -
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Residues in contact with ARG 310 (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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142B GLU* 2.5 37.4 + - - -
271B LYS* 3.4 33.7 - - - +
272B LYS 2.9 29.2 + - - +
273B PRO* 3.9 3.7 - - + +
274B THR* 4.4 11.1 - - - +
278B LYS* 4.7 6.1 - - - +
296B ASP* 2.7 38.6 + - - +
297B VAL 3.2 14.8 - - - +
298B SER* 3.6 15.4 - - - +
309B GLY* 1.3 72.6 - - - +
311B ALA* 1.3 64.0 + - - +
312B VAL* 4.9 2.9 - - + -
333B TYR* 3.9 2.6 - - + +
334B GLY* 3.4 2.4 - - - -
335B ILE* 2.8 48.6 + - + +
1818B PO4 4.1 0.8 + - - -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU 3.9 0.9 - - - +
296B ASP* 3.5 1.9 - - - -
297B VAL* 2.9 41.6 + - + +
310B ARG* 1.3 75.5 - - - +
312B VAL* 1.3 63.8 + - - +
333B TYR* 3.1 11.2 - - - +
334B GLY* 4.8 2.7 - - - -
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ALA* 3.9 36.1 - - + +
242B ILE* 4.4 9.9 - - + -
271B LYS* 4.5 5.6 - - + -
294B GLU* 4.5 2.9 - - + -
295B LEU 3.1 14.6 - - - +
296B ASP* 3.8 25.1 - - + +
310B ARG* 4.8 3.4 - - + +
311B ALA* 1.3 81.3 - - - +
313B ALA* 1.3 74.0 + - - +
331B VAL* 4.4 0.8 - - + +
332B TYR* 3.3 4.2 - - - +
333B TYR* 2.8 56.0 + - + +
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Residues in contact with ALA 313 (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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294B GLU* 3.3 2.3 - - - -
295B LEU* 2.8 45.7 + - + +
312B VAL* 1.3 78.7 - - - +
314B ALA* 1.3 63.6 + - - +
331B VAL* 3.1 11.2 - - - +
332B TYR* 3.7 20.0 - - + -
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Residues in contact with ALA 314 (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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241B ALA* 4.0 22.2 - - + -
292B ARG* 4.3 11.2 - - - +
293B SER* 3.3 11.0 - - - +
294B GLU* 4.2 6.3 - - + -
313B ALA* 1.3 78.2 - - - +
315B TYR* 1.3 62.7 + - - +
330B SER* 3.7 1.4 - - - -
331B VAL* 2.8 52.1 + - + +
332B TYR* 5.6 1.6 - - - -
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Residues in contact with TYR 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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291B TYR 5.6 0.9 - - - -
292B ARG* 3.4 4.6 - - - +
293B SER* 2.8 46.2 + - - +
314B ALA* 1.3 76.8 - - - +
316B GLN* 1.3 67.0 + - - +
317B ASP* 3.4 32.3 + - + -
328B LYS* 3.8 20.2 + - + +
329B THR 3.4 10.1 - - - -
330B SER* 3.6 25.1 - - - -
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Residues in contact with GLN 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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183B ASN* 4.5 10.3 + - - +
239B ASP* 4.6 3.3 - - - +
290B ASN* 2.6 34.4 + - - +
291B TYR 3.4 11.2 - - - +
292B ARG* 3.0 40.4 + - + +
315B TYR* 1.3 81.9 - - - +
317B ASP* 1.3 65.5 + - - +
318B LYS* 4.7 11.5 - - + +
327B ARG 4.2 1.3 - - - -
328B LYS* 3.3 4.2 - - - +
329B THR* 2.7 58.7 + - + +
808B MET* 4.4 5.5 - - - +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP 3.2 4.9 - - - +
291B TYR* 2.9 43.3 + - + +
315B TYR* 3.4 20.4 + - + -
316B GLN* 1.3 74.1 - - - +
318B LYS* 1.3 63.3 + - - +
319B HIS* 4.8 1.9 + - - -
326B GLU* 2.9 24.1 - - - +
327B ARG 3.6 3.1 - - - +
328B LYS* 3.3 30.8 + - - +
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Residues in contact with LYS 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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184B ASN* 5.5 0.4 - - - +
289B ASP 3.4 4.0 - - - -
290B ASN* 3.6 34.3 - - + +
316B GLN* 4.7 10.3 - - + +
317B ASP* 1.3 77.4 + - - +
319B HIS* 1.3 76.2 + - - +
320B SER* 5.1 4.7 - - - -
325B TYR* 4.7 12.1 - - + -
326B GLU* 3.1 6.5 - - - +
327B ARG* 2.9 67.5 + - + +
329B THR* 6.0 0.9 - - + -
1817B PO4 2.9 34.2 + - - -
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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