Contacts of the helix formed by residues 312 - 320 (chain A) in PDB entry 6XYY
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 ASP 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A SER 3.5 4.8 + - - +
311A VAL* 1.3 77.6 - - - +
313A ALA* 1.3 66.4 + - - +
314A LYS* 4.3 9.4 - - + +
315A THR* 2.9 30.1 + - - +
316A ILE* 3.5 2.1 + - - +
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Residues in contact with ALA 313 (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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43A ARG* 3.8 21.2 - - - +
67A VAL* 4.1 10.5 - - + -
91A GLU* 4.0 15.7 - - + +
185A PHE* 3.5 21.7 - - + -
311A VAL 3.4 3.0 + - - -
312A ASP* 1.3 71.6 - - - +
314A LYS* 1.3 58.1 + - - +
315A THR 3.1 0.3 + - - -
316A ILE* 3.1 3.5 + - - +
317A SER* 2.8 30.7 + - - -
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Residues in contact with LYS 314 (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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67A VAL* 5.0 1.5 - - + +
68A GLN 5.6 1.4 + - - -
69A GLU* 3.4 34.0 + - - +
89A VAL* 6.6 0.2 - - + -
312A ASP* 3.2 7.5 - - + +
313A ALA* 1.3 76.5 - - - +
315A THR* 1.3 61.9 + - - +
317A SER* 3.3 6.6 + - - -
318A VAL* 3.1 31.8 + - + +
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Residues in contact with THR 315 (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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289A ASP 5.4 0.4 - - - +
290A CYS* 4.3 11.9 - - + -
311A VAL* 3.5 19.9 - - + +
312A ASP* 2.9 20.8 + - - +
314A LYS* 1.3 76.1 - - - +
316A ILE* 1.3 66.5 + - - +
318A VAL* 3.2 4.0 + - - -
319A GLN* 2.9 46.0 + - + +
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Residues in contact with ILE 316 (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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43A ARG* 3.6 36.3 - - - +
44A PHE* 3.9 21.3 - - + -
184A ALA* 3.9 26.7 - - + -
185A PHE* 3.7 20.6 - - + -
286A LEU* 4.2 14.8 - - + -
290A CYS* 4.4 10.8 - - - -
308A MET* 4.0 10.5 - - + +
311A VAL* 4.2 15.5 - - + +
312A ASP 3.5 1.5 + - - +
313A ALA 3.1 5.7 + - - +
315A THR* 1.3 77.0 - - - +
317A SER* 1.3 64.1 + - - +
320A GLN* 3.1 25.3 + - + +
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Residues in contact with SER 317 (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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67A VAL* 3.5 22.6 - - - +
68A GLN* 3.8 11.0 + - - -
69A GLU* 2.3 37.9 + - - +
185A PHE* 4.0 4.0 - - - -
313A ALA 2.8 17.4 + - - -
314A LYS* 3.6 5.4 - - - -
315A THR 3.2 0.2 - - - -
316A ILE* 1.3 76.7 - - - +
318A VAL* 1.3 57.1 + - - +
320A GLN* 3.4 16.2 + - - +
321A TRP* 3.3 22.9 - - - -
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Residues in contact with VAL 318 (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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69A GLU* 3.7 24.0 - - + +
314A LYS* 3.1 29.2 + - + +
315A THR* 3.8 4.3 - - - +
316A ILE 3.1 0.2 - - - -
317A SER* 1.3 75.6 - - - +
319A GLN* 1.3 81.1 + - + +
320A GLN 3.2 2.0 - - - -
321A TRP* 3.0 26.5 + - - +
322A ASN* 4.3 2.9 + - - +
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Residues in contact with GLN 319 (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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286A LEU* 4.1 12.6 - - + +
289A ASP* 3.9 34.7 + - + +
290A CYS* 4.5 1.6 - - - -
315A THR* 2.9 40.3 + - + +
318A VAL* 1.3 82.1 - - + +
320A GLN* 1.3 65.1 + - - +
321A TRP 3.0 0.7 - - - -
322A ASN* 3.0 49.1 + - - +
323A SER* 4.7 1.4 + - - -
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Residues in contact with GLN 320 (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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67A VAL 5.5 0.8 + - - -
68A GLN* 5.5 5.1 - - - +
153A MET* 3.6 27.8 + - + +
183A GLY* 3.2 11.2 - - - -
184A ALA* 2.6 44.2 + - + +
185A PHE* 4.8 5.6 - - - -
282A ILE* 5.7 0.5 - - - +
286A LEU* 3.9 14.9 - - + +
316A ILE* 3.1 18.5 + - - +
317A SER* 3.4 27.4 + - - +
319A GLN* 1.3 77.7 - - - +
321A TRP* 1.3 71.9 + - + +
322A ASN 3.3 1.4 + - - -
323A SER* 3.4 12.7 + - - -
331A PRO* 3.5 19.5 - - + +
332A SER* 4.2 1.7 + - - -
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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