Contacts of the helix formed by residues 255 - 265 (chain A) in PDB entry 4FV3
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 ASN 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A THR 4.3 8.7 + - - +
180A GLY* 3.8 19.5 - - - -
181A PHE* 3.9 12.2 + - - +
199A ASN* 4.7 9.8 - - + +
253A ILE* 3.4 2.3 - - + +
254A ILE* 1.4 76.9 - - - +
256A LEU* 1.4 57.7 + - - +
257A LYS* 3.4 11.8 + - - +
258A ALA* 3.2 34.3 + - + +
259A ARG* 3.0 27.2 + - - +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ILE 3.1 11.0 + - - +
255A ASN* 1.4 69.5 - - - +
257A LYS* 1.3 57.5 + - + +
259A ARG* 4.5 12.3 - - + +
260A ASN* 2.8 64.3 + - - +
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 3.8 27.7 - - + +
255A ASN* 3.4 10.3 + - - +
256A LEU* 1.3 76.5 - - + +
258A ALA* 1.3 56.8 + - - +
260A ASN* 4.0 3.6 - - - +
261A TYR* 3.1 29.3 + - - +
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 3.7 15.4 - - + +
198A LEU* 3.3 36.9 - - + +
253A ILE* 3.6 20.6 - - + -
255A ASN* 3.2 12.8 + - + +
257A LYS* 1.3 76.1 - - - +
259A ARG* 1.4 63.8 + - - +
261A TYR* 3.4 3.8 + - - +
262A LEU* 3.3 27.0 + - - +
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU* 3.2 26.6 + - + +
251A ASN* 3.0 44.0 + - - +
253A ILE* 2.7 32.0 + - - +
254A ILE* 4.0 12.0 + - - +
255A ASN 3.0 18.2 + - - +
256A LEU* 3.9 13.9 - - - +
258A ALA* 1.4 73.8 - - - +
260A ASN* 1.3 62.7 + - - +
262A LEU* 3.3 9.9 + - - +
263A LEU* 3.0 47.2 + - + +
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Residues in contact with ASN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 2.8 48.4 + - - +
257A LYS* 4.4 3.4 - - - +
259A ARG* 1.3 70.0 - - - +
261A TYR* 1.3 65.4 - - - +
263A LEU* 3.8 20.8 - - - +
264A SER* 3.1 24.3 + - - -
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Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 3.4 30.1 - + + -
198A LEU* 4.8 0.2 - - + -
232A LEU* 3.8 23.6 - - + +
235A LEU* 3.8 26.2 - - + -
236A ASN* 2.8 29.3 + - - -
257A LYS 3.1 20.8 + - - +
258A ALA 3.7 4.3 - - - +
259A ARG 3.3 0.2 - - - -
260A ASN* 1.3 76.5 - - - +
262A LEU* 1.3 66.9 + - + +
264A SER* 2.6 28.5 + - - -
265A LEU* 3.5 37.7 - - + +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 3.8 25.1 - - + -
235A LEU* 4.5 2.2 - - + -
239A LEU* 3.8 31.6 - - + -
245A PRO* 4.4 17.1 - - + +
250A LEU* 3.7 22.9 - - + -
253A ILE* 3.6 31.2 - - + -
258A ALA 3.3 15.2 + - - +
259A ARG* 3.3 8.3 + - - +
261A TYR* 1.3 78.8 - - + +
263A LEU* 1.3 61.0 + - - +
265A LEU* 3.5 24.9 + - + +
294A PHE* 4.2 6.1 - - + -
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU* 4.0 25.8 - - + -
259A ARG* 3.0 34.6 + - + +
260A ASN* 3.8 25.8 - - - +
261A TYR 3.3 0.2 - - - -
262A LEU* 1.3 75.7 - - - +
264A SER* 1.4 60.3 + - - +
265A LEU 3.5 5.9 + - - +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASN 3.1 13.6 + - - -
261A TYR* 2.6 30.2 + - - -
263A LEU* 1.4 73.5 - - - +
265A LEU* 1.3 65.6 + - - +
266A PRO* 3.9 3.6 - - - +
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASN* 4.7 3.1 - - - +
239A LEU* 3.5 31.4 - - + -
244A SER* 5.4 0.4 + - - +
261A TYR* 3.5 50.5 - - + +
262A LEU* 3.7 17.3 - - + +
263A LEU 3.3 8.0 - - - +
264A SER* 1.3 82.6 - - - +
266A PRO* 1.4 80.6 - - + +
267A HIS 3.7 0.2 + - - -
268A LYS* 4.2 17.9 - - - +
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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