Contacts of the strand formed by residues 253 - 257 (chain A) in PDB entry 1SOX
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 GLY 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A PHE 3.2 14.1 - - - -
241A GLU* 4.4 3.8 - - - -
251A PRO 3.4 4.1 + - - -
252A TYR* 1.3 88.8 - - - +
254A ALA* 1.3 64.5 + - - +
300A VAL* 4.5 1.1 - - - -
313A SER* 4.6 0.9 - - - -
315A SER* 3.2 32.5 + - - -
317A TRP* 4.1 9.5 - - - +
318A GLN 4.4 1.7 + - - -
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Residues in contact with ALA 254 (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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239A CYS* 3.5 1.0 - - - -
240A PHE* 2.8 32.5 + - - +
252A TYR* 4.6 0.2 - - + -
253A GLY* 1.3 76.2 - - - +
255A SER* 1.3 63.5 + - - +
297A ALA 3.9 15.0 - - - +
298A ARG* 3.9 17.9 - - - +
300A VAL* 3.8 19.6 - - + +
313A SER* 3.7 9.5 + - - -
318A GLN* 3.2 15.3 - - - +
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Residues in contact with SER 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A HIS* 4.4 6.9 + - - +
238A VAL 3.1 18.8 - - - -
239A CYS* 3.7 9.0 - - - -
240A PHE* 4.5 3.1 - - - -
254A ALA* 1.3 78.0 - - - +
256A ILE* 1.3 65.5 + - - +
298A ARG* 3.8 4.8 - - - -
312A GLU* 3.7 8.5 - - - +
313A SER* 2.8 31.7 + - - -
318A GLN* 2.8 20.2 + - - +
343A GLN* 3.1 17.2 - - - +
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Residues in contact with ILE 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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219A LEU* 4.3 0.2 - - + -
237A HIS* 3.5 7.2 - - - -
238A VAL* 2.9 24.7 + - + +
240A PHE* 4.0 26.0 - - + -
255A SER* 1.3 78.0 - - - +
257A PRO* 1.3 77.6 - - + +
260A ARG* 4.4 6.3 - - + -
261A ALA* 3.8 35.4 - - + +
268A VAL* 4.2 22.0 - - + -
291A VAL* 3.9 29.2 - - + -
298A ARG* 4.3 6.1 - - + -
343A GLN* 4.0 12.6 - - - +
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Residues in contact with PRO 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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236A TRP 3.7 7.9 - - - +
237A HIS* 3.9 15.2 - - + +
256A ILE* 1.3 94.5 - - + +
258A TYR* 1.3 65.7 + - - +
259A GLY* 4.3 5.4 - - - +
260A ARG* 3.2 24.5 + - + +
261A ALA* 3.3 8.8 + - - +
343A GLN* 4.3 21.3 - - + +
404B PRO* 6.2 7.2 - - + -
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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