Contacts of the helix formed by residues 341 - 349 (chain A) in PDB entry 2XAF
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 PRO 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A GLN* 5.3 1.6 - - - +
182A ARG* 3.7 18.8 - - - +
264A PHE* 4.4 14.4 - - + -
339A GLY 3.5 8.7 - - - +
340A ASN* 1.4 83.8 - - - +
342A MET* 1.3 56.6 + - + +
344A VAL* 2.8 30.2 + - + +
345A VAL* 3.5 6.4 + - - +
560A PHE* 3.6 13.2 - - + -
812A HIS* 3.8 18.2 - - + +
815A LEU* 4.2 20.4 - - + -
816A LEU* 3.7 25.8 - - + -
819A LEU* 6.1 0.9 - - + -
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Residues in contact with MET 342 (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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334A VAL* 4.4 13.5 - - + -
337A LEU* 5.3 1.1 - - - -
340A ASN* 2.5 31.5 + - - +
341A PRO* 1.3 69.1 - - - +
343A ALA* 1.3 51.2 + - - +
345A VAL* 3.6 29.6 - - + +
346A SER* 2.6 41.2 + - - -
351A MET* 4.7 7.4 - - + +
571A TYR* 3.6 36.1 - - + +
574A VAL* 4.6 9.0 - - + -
811A VAL* 3.8 17.9 - - + -
812A HIS* 3.8 22.9 - - + +
815A LEU* 4.6 11.7 - - - -
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Residues in contact with ALA 343 (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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180A GLN* 3.4 18.8 - - - +
337A LEU* 3.8 33.7 - - + +
340A ASN* 2.7 24.6 + - - +
342A MET* 1.3 67.6 - - - +
344A VAL* 1.3 58.4 + - + +
346A SER* 2.1 26.7 + - - -
347A LYS* 3.6 13.9 + - - +
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Residues in contact with VAL 344 (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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180A GLN* 4.9 7.9 - - - +
221A TRP* 4.0 9.4 - - + +
222A LEU* 3.7 29.6 - - + -
225A PRO* 3.8 27.1 - - + -
264A PHE* 4.2 21.3 - - + -
341A PRO* 2.8 13.8 + - + +
343A ALA* 1.3 72.8 - - - +
345A VAL* 1.3 68.8 + - + +
346A SER 3.0 1.3 - - - -
347A LYS* 2.9 19.9 + - + +
348A GLN* 3.0 25.4 + - - +
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Residues in contact with VAL 345 (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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264A PHE* 5.0 9.0 - - + -
265A GLY* 5.4 6.1 - - - -
341A PRO 3.5 10.9 + - - +
342A MET* 3.1 27.7 + - + +
344A VAL* 1.3 77.0 - - - +
346A SER* 1.3 54.2 + - - +
348A GLN* 2.8 15.4 + - - +
349A VAL* 2.7 44.7 + - + +
351A MET* 4.6 0.9 - - - -
574A VAL* 3.8 33.4 - - + -
578A LEU* 5.8 9.2 - - + -
815A LEU* 4.5 16.6 - - + -
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Residues in contact with SER 346 (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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337A LEU* 5.0 3.8 - - - +
342A MET 2.6 16.5 + - - -
343A ALA* 2.1 37.1 + - - -
345A VAL* 1.3 73.2 - - - +
347A LYS* 1.3 54.5 + - - +
349A VAL 2.7 20.8 - - - +
351A MET* 3.3 30.4 + - - +
353A LEU* 4.2 20.1 - - - +
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Residues in contact with LYS 347 (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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222A LEU 4.6 6.5 + - - +
223A ASP* 4.4 16.6 + - - +
225A PRO* 4.1 25.4 - - + +
226A LYS* 3.7 21.6 + - + +
343A ALA 3.9 11.0 - - - +
344A VAL* 2.9 10.3 + - - +
346A SER* 1.3 78.8 + - - +
348A GLN* 1.3 64.4 + - - +
349A VAL 3.5 1.7 + - - +
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Residues in contact with GLN 348 (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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221A TRP* 3.3 13.9 - - - -
225A PRO* 2.8 31.6 + - + +
226A LYS* 3.9 19.9 - - - +
264A PHE 3.1 20.5 + - - -
265A GLY* 3.4 6.9 - - - -
266A ILE* 2.5 53.9 + - + +
344A VAL* 3.0 20.8 + - + +
345A VAL* 2.8 16.1 + - - +
347A LYS* 1.3 78.8 - - - +
349A VAL* 1.3 65.1 + - + +
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Residues in contact with VAL 349 (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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266A ILE* 3.9 26.5 - - + -
345A VAL* 2.7 32.3 + - + +
346A SER 2.7 25.5 - - - +
347A LYS 4.2 2.1 - - - +
348A GLN* 1.3 83.3 - - + +
350A ASN* 1.3 73.0 + - + +
351A MET* 2.9 12.7 + - + +
573A CYS* 4.0 18.6 - - + +
574A VAL* 4.9 4.5 - - + +
577A ALA* 3.9 19.3 - - + -
578A LEU* 6.0 0.2 - - + -
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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