Contacts of the helix formed by residues 256 - 264 (chain E) in PDB entry 3W13
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 PHE 256 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244E PRO 4.2 2.9 + - - +
246E TYR* 3.8 31.3 - + + +
255E ASN* 1.3 73.2 - - - +
257E SER* 1.3 67.9 + - - +
259E CYS* 3.1 7.3 + - - +
260E GLN* 2.9 57.5 + - + +
279E ILE* 3.8 22.2 - - + -
297E SER 5.6 1.1 - - - -
298E ASN* 3.6 30.7 - - + -
299E LEU* 3.9 7.4 - - + -
300E LEU* 5.8 2.0 - - + -
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Residues in contact with SER 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E ASN* 3.0 13.4 + - - +
256E PHE* 1.3 81.8 - - - +
258E PHE* 1.3 63.7 + - - +
260E GLN* 3.3 7.3 + - - +
261E ASP* 3.0 41.7 + - - +
1H NAG 4.3 20.2 + - - +
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Residues in contact with PHE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E PHE* 3.9 22.7 - + - -
252E ARG* 4.0 26.2 - - - -
254E VAL* 3.5 38.4 - - + -
255E ASN* 2.8 24.0 + - - +
257E SER* 1.3 74.6 - - - +
259E CYS* 1.3 67.9 + - - +
261E ASP* 3.3 14.3 + - - +
262E LEU* 3.3 49.1 + - + +
284E CYS* 5.5 0.7 - - - -
1H NAG 4.3 22.4 - - - +
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Residues in contact with CYS 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E TYR* 5.4 2.5 - - + -
254E VAL* 5.0 1.8 - - + -
255E ASN 3.4 7.7 + - - +
256E PHE* 3.1 12.9 + - - +
258E PHE* 1.3 86.2 - - + +
260E GLN* 1.3 61.4 + - - +
262E LEU* 3.5 5.4 + - - +
263E HIS* 3.2 20.1 + - - +
277E TYR* 4.0 10.2 - - - +
278E VAL 4.5 2.2 - - - -
279E ILE* 4.0 24.0 - - + -
284E CYS* 2.0 55.2 - - + -
299E LEU* 4.8 1.7 - - - +
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Residues in contact with GLN 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E PHE* 2.9 37.4 + - + +
257E SER* 3.5 10.8 - - - +
259E CYS* 1.3 74.7 - - - +
261E ASP* 1.3 72.6 + - - +
263E HIS* 3.0 13.0 + - - +
264E HIS* 3.2 42.9 + - + +
299E LEU* 3.6 32.6 - - + +
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Residues in contact with ASP 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E SER* 3.0 31.6 + - - +
258E PHE* 3.6 8.0 - - - +
260E GLN* 1.3 83.7 + - - +
262E LEU* 1.3 67.3 + - + +
264E HIS* 3.6 20.5 + - - +
265E LYS 5.5 0.2 - - - -
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Residues in contact with LEU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E PHE* 4.6 7.6 - - + -
258E PHE* 3.3 57.3 + - + +
259E CYS* 3.8 8.3 - - - +
260E GLN 3.2 0.6 - - - -
261E ASP* 1.3 82.4 - - + +
263E HIS* 1.3 67.5 + - - +
264E HIS 3.4 0.7 + - - -
265E LYS 3.6 15.4 - - - +
276E GLN* 5.9 0.2 - - - -
277E TYR* 3.8 33.8 - - + +
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Residues in contact with HIS 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E CYS 3.2 9.9 + - - +
260E GLN 3.0 10.2 + - - +
262E LEU* 1.3 79.5 - - - +
264E HIS* 1.3 78.6 + + - +
265E LYS* 2.9 10.9 + - - +
276E GLN* 3.4 44.1 + - + +
277E TYR* 2.8 41.6 - - - +
294E MET* 3.6 23.7 - - + +
299E LEU* 3.6 23.1 - - + +
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Residues in contact with HIS 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E GLN* 3.2 51.2 + - + +
261E ASP* 3.6 14.1 - - - +
262E LEU 3.3 1.0 - - - -
263E HIS* 1.3 90.3 + + - +
265E LYS* 1.3 70.7 + - - +
299E LEU* 5.4 2.5 - - + -
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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