Contacts of the strand formed by residues 277 - 285 (chain B) in PDB entry 3V4K
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 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B VAL* 4.0 14.1 - - + -
225B GLU 3.2 15.3 - - - +
226B ARG* 3.7 30.7 + - + -
232B TRP* 3.5 5.0 - - - -
235B LEU* 4.0 7.4 - - + -
271B LEU* 3.5 39.7 - - + +
272B ASP* 2.9 51.1 + - - +
275B GLN* 3.6 16.7 - - + +
276B ASP* 1.3 75.9 - - - +
278B ARG* 1.3 54.8 + - - +
279B VAL* 4.6 5.6 - - + -
304B HIS* 2.9 26.3 + + - +
305B VAL* 4.6 2.0 - - - -
306B SER* 2.8 35.3 + - - -
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Residues in contact with ARG 278 (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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223B GLU 3.9 0.7 - - - +
224B VAL* 3.4 3.1 - - - -
225B GLU* 2.7 73.2 + - - +
232B TRP* 3.4 55.6 - - + +
277B TYR* 1.3 73.0 - - - +
279B VAL* 1.3 63.4 + - - +
280B THR* 4.0 8.1 + - - +
306B SER* 3.3 12.8 - - - +
308B CYS* 3.9 28.5 - - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B TYR* 5.1 0.9 - - + -
223B GLU 3.6 9.0 - - - +
224B VAL* 4.2 10.5 - - + -
262B PHE* 3.4 36.8 - - + -
266B ILE* 5.0 3.1 - - + -
269B TRP* 4.1 26.9 - - + -
271B LEU* 5.1 1.1 - - + -
277B TYR* 4.6 5.6 - - + -
278B ARG* 1.3 74.8 - - - +
280B THR* 1.3 62.9 + - - +
305B VAL* 3.8 29.8 - - + -
306B SER 2.9 8.8 + - - +
307B LEU* 3.5 7.9 - - + +
308B CYS* 2.9 25.1 + - - +
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B CYS 3.8 0.3 - - - +
222B TYR* 3.2 5.9 - - - +
223B GLU* 3.0 45.6 + - - +
225B GLU* 4.3 8.7 + - - -
278B ARG* 4.0 13.9 + - - +
279B VAL* 1.3 73.9 - - - +
281B CYS* 1.3 62.8 + - - +
282B PHE* 3.7 29.7 - - + -
308B CYS* 3.4 16.7 - - + +
310B LYS* 4.0 27.6 + - + +
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Residues in contact with CYS 281 (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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220B LEU* 4.0 12.3 - - + -
221B CYS 3.2 6.1 - - - +
222B TYR* 4.5 0.2 - - - -
262B PHE* 3.1 50.5 - - - -
280B THR* 1.3 76.7 - - - +
282B PHE* 1.3 58.1 + - - +
283B THR* 3.8 17.8 + - + +
295B MET* 5.4 2.2 - - + -
307B LEU* 4.1 9.2 - - - -
308B CYS 2.9 9.8 + - - +
309B ILE* 3.5 7.7 - - + -
310B LYS* 2.8 31.9 + - - +
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Residues in contact with PHE 282 (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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206B PHE* 3.9 7.2 - - + -
219B TYR 3.8 1.2 - - - +
220B LEU* 3.4 1.4 - - - -
221B CYS* 2.8 48.4 + - + +
223B GLU* 3.8 26.9 - - + -
280B THR* 3.7 21.8 - - + -
281B CYS* 1.3 69.5 - - - +
283B THR* 1.3 61.3 + - - +
310B LYS* 3.2 39.3 - - + +
338B MET* 4.1 14.4 - - + -
342B GLU* 4.2 15.3 - - + -
345B HIS* 3.7 23.8 - + - -
346B CYS* 3.2 33.4 - - - -
350B PHE* 4.1 8.7 - + - -
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Residues in contact with THR 283 (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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206B PHE* 3.8 5.3 - - - -
218B THR* 4.9 3.4 - - + -
219B TYR 3.3 5.6 - - - -
220B LEU* 3.8 31.2 - - + -
259B GLU* 5.6 4.0 - - + +
281B CYS* 4.0 14.1 - - + +
282B PHE* 1.3 78.4 - - - +
284B SER* 1.3 60.2 + - - +
285B TRP 3.0 21.4 + - - +
287B PRO* 6.2 1.1 - - + -
295B MET* 6.5 0.9 - - + -
309B ILE* 3.9 13.1 - - + +
310B LYS 2.9 5.8 + - - -
311B THR* 3.1 17.3 + - - -
312B ALA* 2.8 26.7 + - - +
338B MET* 4.1 0.2 - - - +
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Residues in contact with SER 284 (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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205B ASN* 3.2 33.2 - - - +
206B PHE* 3.8 15.4 - - - -
217B GLU 3.9 5.5 + - - -
218B THR* 3.6 6.8 - - - -
219B TYR* 2.9 34.0 + - - +
283B THR* 1.3 75.0 - - - +
285B TRP* 1.3 60.8 + - - +
311B THR* 4.0 0.2 - - - -
312B ALA* 3.5 4.5 - - - +
313B ARG* 3.3 37.4 + - - +
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Residues in contact with TRP 285 (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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2B CL 3.7 21.1 - - + -
215B ARG* 2.8 31.3 + - - -
216B HIS 4.8 1.9 - - - -
217B GLU 3.2 19.9 + - - -
218B THR* 3.5 26.0 - - + +
259B GLU* 4.2 1.7 - - - +
283B THR* 3.0 18.2 + - - -
284B SER* 1.3 76.5 + - - +
286B SER* 1.3 70.9 + - - +
287B PRO* 4.1 0.3 - - - +
311B THR* 3.1 7.2 - - - -
313B ARG* 3.2 57.8 - - + +
314B ILE 3.4 23.8 - - - -
315B TYR* 3.8 25.4 - + + -
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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