Contacts of the strand formed by residues 307 - 311 (chain A) in PDB entry 2XIJ
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 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER* 4.5 3.0 + - - -
261A ILE* 3.1 46.4 - - + +
280A THR* 3.9 11.9 - - + -
281A LEU* 3.8 22.4 - - + -
305A LEU* 4.9 5.2 - - + -
306A SER* 1.3 86.1 + - - +
308A PHE* 1.3 61.9 - - - +
309A TRP* 4.2 9.4 - + + -
329A TRP* 3.7 43.1 - + - -
346A LEU 5.0 0.9 - - - -
347A LEU* 3.5 43.3 - - + -
348A ARG 2.9 8.7 + - - +
349A ALA* 3.4 3.8 - - + -
350A HIS* 2.9 27.8 + - - +
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Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR* 6.3 0.7 - - + -
218A GLN* 4.1 5.2 - - - -
260A SER* 3.9 9.4 - - - +
261A ILE 2.9 7.7 + - - -
262A SER* 3.6 25.8 - - - +
263A GLY* 2.7 32.2 + - - -
264A TYR* 3.1 37.1 + + + -
265A HIS* 3.7 22.0 - + - -
307A PHE* 1.3 75.2 - - - +
309A TRP* 1.3 64.7 + - - +
350A HIS* 3.2 33.7 - + + -
352A GLN* 3.6 31.0 - - + -
1754A EDO 4.1 13.7 - - - +
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Residues in contact with TRP 309 (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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263A GLY* 4.5 0.2 - - - -
264A TYR* 4.0 3.8 - - - -
276A GLU* 3.5 25.8 - - + +
277A LEU* 3.6 33.7 - - + -
280A THR* 3.6 37.2 - - + -
281A LEU* 4.1 8.1 - - + -
307A PHE* 4.6 5.4 - + + -
308A PHE* 1.3 84.0 - - - +
310A GLY* 1.3 66.0 + - - +
311A ILE* 4.7 1.3 - - + -
321A LYS* 4.3 14.1 - - - +
322A MET* 4.0 29.0 + - + +
325A GLY* 4.9 2.5 - - - -
347A LEU* 4.2 29.0 - - + +
349A ALA* 3.6 30.8 - - + +
350A HIS 2.8 6.5 + - - -
351A CYS* 3.2 15.7 - - - -
352A GLN 3.0 24.9 + - - -
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Residues in contact with GLY 310 (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 TYR* 3.5 21.6 - - - +
267A GLN* 3.2 17.4 + - - -
276A GLU* 2.9 11.6 + - - -
309A TRP* 1.3 73.3 - - - +
311A ILE* 1.3 65.5 + - - +
321A LYS* 2.7 29.3 + - - -
352A GLN 3.5 6.7 - - - -
354A SER* 5.7 0.4 - - - -
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Residues in contact with ILE 311 (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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267A GLN* 3.9 1.7 + - - +
309A TRP* 4.7 0.9 - - + -
310A GLY* 1.3 82.2 - - - +
312A GLY* 1.3 66.6 + - - +
318A GLU* 3.6 18.8 - - + +
321A LYS* 4.6 1.3 - - - +
322A MET* 3.8 20.6 - - + -
351A CYS* 3.8 37.9 - - + -
352A GLN 3.1 10.5 + - - +
353A THR* 3.5 5.7 - - + -
354A SER 2.9 25.2 + - - +
373A GLU* 3.3 38.0 - - - +
376A ALA* 3.9 15.9 - - + -
377A ALA* 4.0 8.5 - - + -
385A LEU* 5.5 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