Contacts of the helix formed by residues 258 - 264 (chain K) in PDB entry 3V3K
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 258 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240K PRO* 3.8 16.4 - - + +
241K GLY* 3.3 22.9 + - - +
242K ALA* 4.2 4.5 - - - +
243K VAL* 4.7 6.3 - - + -
256K VAL 3.8 0.4 + - - -
257K SER* 1.3 69.7 - - - +
259K GLU* 1.3 67.6 + - - +
261K ILE* 3.2 10.2 + - + +
262K VAL* 3.0 34.9 + - + +
282K ILE* 3.3 44.9 - - + -
329K VAL* 3.9 9.4 - - + -
331K TYR* 3.8 16.4 - - + +
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Residues in contact with GLU 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240K PHE* 3.0 113.5 + - + +
241K GLY 4.7 0.4 + - - -
257K SER* 3.9 12.3 - - - +
258K VAL* 1.3 75.7 - - - +
260K LYS* 1.3 62.0 + - - +
262K VAL* 3.7 1.4 + - - +
263K ASN* 3.0 38.6 + - - +
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Residues in contact with LYS 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H GLU* 2.7 30.2 + - - -
212K VAL* 4.4 24.2 - - + +
256K VAL* 4.9 8.3 - - + -
257K SER* 3.2 24.5 + - - +
259K GLU* 1.3 77.7 - - - +
261K ILE* 1.3 65.8 + - - +
263K ASN* 3.6 5.7 + - - +
264K ILE* 3.4 29.5 + - + +
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Residues in contact with ILE 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K MET* 4.9 1.3 - - + -
215K LEU* 3.4 35.0 - - + -
232K VAL* 4.9 0.2 - - + -
234K ILE* 3.4 31.4 - - + -
243K VAL* 3.8 20.2 - - + -
256K VAL* 3.6 19.1 - - + -
257K SER 3.2 17.0 + - - +
258K VAL* 3.2 13.1 + - + +
260K LYS* 1.3 75.8 - - + +
262K VAL* 1.3 63.3 + - + +
264K ILE* 3.6 14.2 - - + +
265K PHE* 3.3 19.8 - - - -
280K PHE* 4.1 17.5 - - + -
282K ILE* 6.0 1.1 - - + -
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Residues in contact with VAL 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334I PHE* 5.6 0.9 - - + -
240K PHE* 3.7 18.6 - - - +
258K VAL* 3.0 29.8 + - + +
259K GLU 4.2 1.3 - - - +
261K ILE* 1.3 75.9 - - + +
263K ASN* 1.3 59.4 + - - +
264K ILE 3.2 1.8 - - - -
265K PHE* 3.1 22.3 + - - +
266K ASN* 3.7 7.0 + - + +
280K PHE* 3.8 22.7 - - + -
327K ILE* 3.3 40.1 - - + +
329K VAL* 3.7 24.5 - - + -
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Residues in contact with ASN 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334I PHE* 5.1 6.1 - - - -
240K GLN* 3.0 41.0 - - - +
259K GLU* 3.0 27.1 + - - +
260K LYS* 3.6 5.8 + - - +
262K VAL* 1.3 76.5 - - - +
264K ILE* 1.3 59.7 + - - +
265K PHE 3.2 0.4 - - - -
266K ASN* 3.0 42.6 + - - +
269K SER* 3.4 7.3 + - - -
324K PRO* 5.6 2.3 - - - +
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Residues in contact with ILE 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K VAL* 4.4 15.3 - - + +
215K LEU* 3.9 31.0 - - + +
216K LEU* 4.0 28.9 - - + -
219K ALA* 3.5 30.5 - - + +
260K LYS* 3.4 22.9 + - + +
261K ILE* 3.6 15.5 - - + +
262K VAL 3.2 0.6 - - - -
263K ASN* 1.3 77.1 - - - +
265K PHE* 1.3 62.2 + - + +
266K ASN 3.5 0.2 - - - -
269K SER* 3.1 22.5 - - - -
270K CYS 3.9 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