Contacts of the helix formed by residues 257 - 266 (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 HIS 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ZN 2.0 39.6 - - - -
244B ASN* 4.1 9.9 - - + -
254B GLU* 4.9 9.8 - - + +
255B GLY 3.4 15.3 + - - -
256B ARG* 1.3 77.9 - - - +
258B ALA* 1.3 65.0 + - - +
259B GLU* 3.6 5.1 + - - +
260B LEU* 3.0 20.4 + - + +
261B CYS* 3.2 11.2 + - - +
288B CYS* 3.8 12.8 - - + -
290B SER* 5.5 0.9 - - - -
291B CYS* 3.6 12.7 - - - -
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Residues in contact with ALA 258 (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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218B THR* 3.7 31.4 - - + +
220B LEU* 4.4 7.9 - - + -
242B LEU* 3.3 26.5 - - + +
243B ALA* 4.1 2.0 - - - -
244B ASN* 3.7 29.5 - - - +
257B HIS* 1.3 72.5 - - - +
259B GLU* 1.3 64.5 + - - +
261B CYS* 3.3 2.8 + - - -
262B PHE* 3.0 20.1 + - - +
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Residues in contact with GLU 259 (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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4B ZN 4.0 2.5 - - - -
218B THR* 3.9 23.6 + - - +
220B LEU* 4.3 12.8 - - + -
257B HIS* 3.6 11.1 - - - +
258B ALA* 1.3 87.6 + - - +
260B LEU* 1.3 61.0 + - - +
262B PHE* 3.4 10.6 - - - +
263B LEU* 3.1 30.9 + - - +
283B THR* 5.6 3.6 - - + +
285B TRP 4.2 1.7 - - - +
286B SER 4.1 3.5 - - - +
287B PRO* 3.4 32.7 - - + +
288B CYS 4.6 0.6 + - - -
291B CYS* 3.8 20.6 - - + -
295B MET* 3.9 26.6 - - + +
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Residues in contact with LEU 260 (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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256B ARG* 3.7 41.2 + - + +
257B HIS* 3.0 15.6 + - + +
259B GLU* 1.3 77.4 - - + +
261B CYS* 1.3 60.0 + - - +
263B LEU* 3.2 10.7 + - + +
264B ASP* 2.9 34.1 + - - +
290B SER 5.6 0.2 - - - -
291B CYS* 3.9 25.8 - - - -
294B GLU* 4.0 32.3 - - + -
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Residues in contact with CYS 261 (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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242B LEU* 4.2 18.8 - - + -
243B ALA 4.8 4.5 - - - +
245B GLN* 4.1 25.8 - - - -
256B ARG* 4.0 23.1 - - - -
257B HIS 3.2 11.2 + - - +
258B ALA* 3.5 8.3 - - - +
260B LEU* 1.3 77.4 - - - +
262B PHE* 1.3 61.5 + - - +
264B ASP* 3.2 20.7 + - - +
265B VAL* 3.2 20.0 + - + +
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Residues in contact with PHE 262 (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* 3.9 29.8 - - + -
222B TYR* 3.8 22.2 - + + -
242B LEU* 4.0 8.7 - - + +
258B ALA 3.0 13.4 + - - +
259B GLU 3.4 11.7 - - - +
260B LEU 3.2 0.2 - - - -
261B CYS* 1.3 76.0 - - - +
263B LEU* 1.3 74.6 + - + +
265B VAL* 3.2 23.7 + - + +
266B ILE* 3.4 25.4 - - + +
269B TRP* 4.1 11.9 - + - -
279B VAL* 3.4 24.0 - - + -
281B CYS* 3.1 34.1 - - - -
295B MET* 4.6 9.9 - - + -
307B LEU* 4.0 12.8 - - + -
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Residues in contact with LEU 263 (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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259B GLU 3.1 14.4 + - - +
260B LEU* 3.2 13.7 + - + +
262B PHE* 1.3 91.6 - - + +
264B ASP* 1.3 64.9 + - - +
266B ILE* 3.5 10.8 + - + +
267B PRO* 3.3 19.2 - - - +
294B GLU* 3.9 18.8 - - + +
295B MET* 3.9 40.2 - - + +
298B PHE* 3.9 39.3 - - + -
299B ILE* 6.2 0.2 - - + -
307B LEU* 6.0 2.2 - - + -
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Residues in contact with ASP 264 (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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256B ARG* 2.8 43.3 + - - -
260B LEU 2.9 20.0 + - - +
261B CYS* 3.3 14.7 - - - +
262B PHE 3.1 0.2 - - - -
263B LEU* 1.3 79.3 - - - +
265B VAL* 1.3 63.9 + - + +
267B PRO* 3.4 10.8 - - - +
268B PHE* 3.5 18.6 - - + -
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Residues in contact with VAL 265 (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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222B TYR* 4.8 13.5 - - + +
242B LEU* 4.9 8.3 - - + -
261B CYS* 3.2 13.6 + - + +
262B PHE* 3.2 23.6 - - + +
264B ASP* 1.3 78.8 - - + +
266B ILE* 1.3 66.8 + - - +
267B PRO 3.3 0.4 - - - -
268B PHE* 2.9 28.2 + - + +
269B TRP* 3.7 30.3 + - + +
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Residues in contact with ILE 266 (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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262B PHE* 3.4 43.0 + - + +
263B LEU* 4.0 8.1 - - + +
264B ASP 3.4 0.2 - - - -
265B VAL* 1.3 76.3 - - - +
267B PRO* 1.3 71.1 - - + +
269B TRP* 3.0 55.6 + - + +
270B LYS 4.2 1.0 + - - -
271B LEU* 4.4 15.5 + - + +
279B VAL* 5.0 5.6 - - + -
298B PHE* 3.7 39.0 - - + -
304B HIS* 5.9 1.3 - - - +
305B VAL* 5.1 6.7 - - + -
307B LEU* 6.1 0.4 - - + -
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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