Contacts of the strand formed by residues 305 - 313 (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 VAL 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ILE* 5.1 6.3 - - + -
271B LEU* 4.1 15.9 - - + -
277B TYR* 3.7 3.4 - - + -
279B VAL* 3.8 26.9 - - + -
298B PHE* 4.6 13.2 - - + -
299B ILE* 4.7 17.6 - - + +
302B ASN* 3.0 24.0 + - + +
303B LYS* 4.2 6.0 - - - +
304B HIS* 1.3 103.9 - - + +
306B SER* 1.3 69.9 + - - +
307B LEU* 4.0 11.1 + - + +
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Residues in contact with SER 306 (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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232B TRP* 4.8 10.2 - - - -
276B ASP* 6.1 0.5 - - - +
277B TYR 2.8 17.7 + - - -
278B ARG* 3.3 15.0 - - - +
279B VAL 2.9 25.3 + - - +
303B LYS 5.5 1.0 + - - -
305B VAL* 1.3 73.4 - - - +
307B LEU* 1.3 60.6 + - - +
308B CYS* 5.7 1.6 - - - -
334B LYS* 5.2 12.6 + - - -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 4.0 27.8 - - + -
263B LEU* 6.0 2.0 - - + -
266B ILE* 6.1 0.4 - - + -
279B VAL* 3.5 18.2 - - + +
281B CYS* 4.1 11.7 - - - -
295B MET* 3.8 27.8 - - + -
299B ILE* 4.0 30.1 - - + +
305B VAL* 3.9 7.1 + - + -
306B SER* 1.3 73.3 - - - +
308B CYS* 1.3 66.2 + - - +
309B ILE* 4.1 16.4 - - + -
328B LEU* 4.5 6.7 - - + -
332B GLY 4.3 3.0 + - - +
333B ALA* 3.4 16.0 - - + +
334B LYS* 3.0 24.8 + - - +
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Residues in contact with CYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 3.9 31.4 - - - -
279B VAL 2.9 7.0 + - - +
280B THR* 3.4 20.6 - - + +
281B CYS* 2.9 27.4 + - - +
306B SER* 4.9 2.2 - - - -
307B LEU* 1.3 79.3 - - - +
309B ILE* 1.3 63.4 + - - +
310B LYS* 4.0 12.8 - - - -
334B LYS* 3.3 30.1 - - - +
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Residues in contact with ILE 309 (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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281B CYS* 3.5 9.4 - - + +
283B THR* 3.9 26.9 - - + +
286B SER* 5.5 0.4 - - - -
287B PRO* 4.6 15.3 - - + -
295B MET* 3.8 21.5 - - + -
307B LEU* 4.1 18.6 - - + -
308B CYS* 1.3 75.5 - - - +
310B LYS* 1.3 62.8 + - - +
311B THR* 4.7 6.1 - - - -
328B LEU* 3.5 33.7 - - + -
333B ALA* 4.7 2.0 - - + -
334B LYS 2.8 11.5 + - - +
335B ILE* 3.3 19.4 - - + +
336B SER* 2.9 27.4 + - - +
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Residues in contact with LYS 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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280B THR* 4.0 20.5 + - + +
281B CYS 2.8 8.0 + - - +
282B PHE* 3.2 38.5 - - + -
283B THR* 2.9 22.8 + - - -
308B CYS* 4.6 11.9 - - - -
309B ILE* 1.3 76.5 - - - +
311B THR* 1.3 58.9 + - - +
334B LYS 5.7 0.2 - - - +
336B SER* 3.4 22.7 - - - +
338B MET* 3.6 15.8 - - + +
342B GLU* 4.1 20.2 + - + +
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Residues in contact with THR 311 (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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283B THR* 3.1 22.2 + - - -
285B TRP 3.1 2.9 - - - -
286B SER* 3.1 23.5 + - - -
309B ILE* 4.7 4.7 - - - -
310B LYS* 1.3 71.5 - - - +
312B ALA* 1.3 63.5 + - - +
313B ARG 2.9 27.9 + - - +
314B ILE* 4.7 2.0 - - + +
335B ILE* 5.2 7.9 - - + -
336B SER 2.9 18.2 + - - +
337B ILE* 3.4 20.9 - - + +
338B MET* 2.8 26.2 + - - +
375B LEU* 6.3 0.4 - - + -
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Residues in contact with ALA 312 (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* 3.6 29.6 - - + +
208B ASN* 3.6 9.2 + - - +
283B THR 2.8 13.2 + - - +
284B SER* 3.5 17.0 - - - +
311B THR* 1.3 74.4 - - - +
313B ARG* 1.3 67.2 + - + +
337B ILE* 4.5 2.6 - - - +
338B MET* 3.7 6.3 - - - -
343B PHE* 3.9 18.5 - - + -
371B LEU* 3.3 20.0 - - - +
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Residues in contact with ARG 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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205B ASN* 2.7 31.3 + - - -
206B PHE* 3.9 3.6 + - - +
207B ASN 2.8 29.2 + - - +
208B ASN* 4.2 9.2 - - + +
209B GLU 5.0 0.2 - - - -
215B ARG* 3.6 44.1 - - - +
217B GLU 4.7 0.8 + - - -
284B SER* 3.3 22.8 + - - +
285B TRP* 3.2 56.6 - - + +
286B SER 3.1 11.8 + - - -
311B THR* 2.9 21.4 + - - +
312B ALA* 1.3 83.5 - - - +
314B ILE* 1.3 61.9 + - - +
337B ILE* 5.3 0.2 - - - -
371B LEU* 4.2 9.9 - - + -
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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