Contacts of the helix formed by residues 253 - 257 (chain A) in PDB entry 6F0X
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 GLN 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ILE 5.3 0.3 - - - +
213A ASN* 4.3 10.8 - - - +
214A SER* 4.2 12.8 + - - +
251A ILE* 3.2 9.2 - - - +
252A ASP* 1.3 112.4 + - - +
254A VAL* 1.3 57.5 + - - +
255A GLU* 3.0 29.2 - - + +
256A SER* 2.7 42.5 + - - -
257A LEU* 3.4 3.1 + - - +
300A ASN* 5.9 2.5 - - - +
261B ARG* 5.8 0.4 - - - +
278B ASN* 3.5 26.3 + - + +
281B LEU* 6.1 0.8 - - - +
282B THR* 3.5 19.9 - - - +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 3.7 16.8 - - + -
251A ILE* 4.2 7.4 + - + +
253A GLN* 1.3 71.8 - - - +
255A GLU* 1.3 57.8 + - - +
257A LEU* 2.6 26.3 + - - +
258A THR* 2.9 10.1 + - - +
297A THR* 3.5 33.7 - - + -
298A THR 3.0 19.4 + - - +
299A SER* 4.4 5.2 - - - +
305A ILE* 3.6 29.6 - - + -
306A ASP* 5.1 1.3 - - + +
309A PHE* 3.7 25.4 - - + -
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP 4.3 0.5 - - - +
253A GLN* 3.0 33.8 - - + +
254A VAL* 1.3 82.2 + - - +
256A SER* 1.3 58.6 + - - +
258A THR* 3.1 19.8 - - + +
259A ALA* 3.0 23.4 + - - +
299A SER* 3.2 32.2 + - - +
300A ASN* 5.3 1.6 + - - +
301A ILE* 4.5 19.0 - - + +
304A LYS* 5.0 3.6 - - + +
305A ILE* 5.6 1.3 - - - +
261B ARG* 4.0 15.6 + - - +
274B ILE* 3.9 30.1 - - + +
278B ASN* 5.8 0.4 - - + -
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Residues in contact with SER 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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214A SER* 2.4 34.3 + - - -
215A HIS 4.0 2.1 + - - -
218A PHE* 4.3 11.6 - - - -
253A GLN* 2.7 25.7 + - - -
255A GLU* 1.3 78.0 - - - +
257A LEU* 1.3 62.9 + - - +
259A ALA* 3.2 20.3 - - - +
277A VAL* 5.9 0.3 - - - +
274B ILE* 6.1 0.4 - - - -
275B ARG* 4.5 11.7 - - - +
278B ASN* 3.8 16.2 + - - -
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Residues in contact with LEU 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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212A ILE* 6.6 0.2 - - + -
214A SER* 4.6 12.6 - - - -
217A LEU* 5.5 4.7 - - + -
218A PHE* 5.3 7.6 - - + -
251A ILE* 3.7 37.9 - - + -
253A GLN 3.4 1.9 + - - +
254A VAL* 2.6 16.3 + - + +
256A SER* 1.3 77.3 - - - +
258A THR* 1.3 55.4 + - - +
259A ALA 3.2 4.9 - - - -
260A ALA* 4.7 2.3 + - - +
277A VAL* 3.5 35.0 - - + +
280A VAL* 4.7 18.8 - - + -
281A LEU* 5.0 6.3 - - + -
284A ILE* 4.9 10.5 - - + -
306A ASP* 4.4 6.6 - - - +
309A PHE* 4.4 28.9 - - + -
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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