Contacts of the helix formed by residues 309 - 316 (chain A) in PDB entry 5Z58
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 ARG 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A PRO* 6.4 0.2 - - - +
307A PRO* 2.7 26.0 + - + +
308A ILE* 1.3 73.7 - - - +
310A THR* 1.3 61.7 + - - +
311A GLU* 3.2 28.1 + - - +
312A TYR* 2.8 58.0 + - + +
313A LYS* 3.4 3.7 + - - +
852C ARG* 6.2 2.2 - - - -
853C ARG* 4.7 2.9 - - - +
886C ASP* 5.2 7.9 - - - +
-12G G 4.5 26.1 + - - -
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Residues in contact with THR 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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271A MET* 3.5 43.5 - - + +
272A ALA 3.8 17.9 - - - +
273A ILE* 5.3 2.0 - - + -
274A PRO* 6.3 0.7 - - + -
308A ILE 4.0 0.4 + - - -
309A ARG* 1.3 74.9 - - - +
311A GLU* 1.3 65.5 + - - +
313A LYS* 3.0 15.4 + - - +
314A ILE* 3.0 26.7 + - + +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.5 22.3 - - + +
273A ILE* 4.9 4.7 - - + -
274A PRO* 4.2 25.0 - - + +
309A ARG* 3.4 37.9 + - - +
310A THR* 1.3 80.8 + - - +
312A TYR* 1.3 57.9 + - + +
314A ILE* 4.5 2.7 - - - +
315A ALA* 2.9 29.3 + - - +
885C THR* 2.8 24.6 - - + +
886C ASP* 5.5 3.8 - - - -
889C THR* 3.7 29.0 - - + +
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Residues in contact with TYR 312 (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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306A GLN* 5.9 0.2 - - + -
307A PRO 4.5 2.0 - - - -
308A ILE* 4.0 19.1 - - + -
309A ARG* 2.8 47.7 + - + +
311A GLU* 1.3 79.6 - - + +
313A LYS* 1.3 58.7 + - - +
315A ALA* 3.2 4.4 + - - +
316A PHE* 2.9 30.3 + + + -
320A TYR* 3.6 28.0 - - + -
853C ARG* 1.8 38.3 + - - -
881C PHE 3.0 11.0 - - - -
882C GLY* 2.4 44.7 + - - -
885C THR* 3.7 13.7 - - + -
886C ASP* 4.0 9.0 - - + +
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Residues in contact with LYS 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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269A LEU* 4.3 4.4 - - + +
271A MET* 3.4 38.4 - - + +
308A ILE* 4.0 32.2 + - + -
309A ARG 3.4 4.2 + - - +
310A THR* 3.0 16.1 + - - +
312A TYR* 1.3 75.4 - - - +
314A ILE* 1.3 59.8 + - - +
317A PRO* 3.1 31.6 - - - +
320A TYR* 3.8 32.3 - - + +
321A ASN* 4.5 10.0 - - - +
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Residues in contact with ILE 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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257A LEU* 4.1 19.3 - - + -
262A ALA* 4.1 22.2 - - + +
265A THR* 3.5 27.6 - - + +
266A SER* 3.7 29.8 - - - -
269A LEU* 4.5 5.4 - - + -
271A MET* 4.1 17.9 - - + -
273A ILE* 3.9 19.3 - - + -
310A THR* 3.0 17.6 + - + +
311A GLU* 4.1 4.3 - - - +
313A LYS* 1.3 75.9 - - - +
315A ALA* 1.3 65.2 + - - +
316A PHE 3.4 0.3 + - - -
317A PRO* 3.6 10.4 - - - +
330A THR* 2.8 17.9 + - - +
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Residues in contact with ALA 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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256A TYR* 3.9 12.1 - - + +
257A LEU* 4.4 7.6 - - + +
311A GLU 2.9 19.5 + - - +
312A TYR 3.2 0.9 + - - +
314A ILE* 1.3 79.7 - - - +
316A PHE* 1.3 82.0 + - + +
317A PRO* 3.3 6.1 - - - +
330A THR* 3.8 22.2 + - - +
331A TRP* 4.6 3.5 - - + +
177C ARG* 3.9 3.3 + - - -
885C THR* 3.4 20.6 - - - +
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Residues in contact with PHE 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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256A TYR* 5.5 0.2 - - - -
312A TYR* 2.9 9.2 + - + -
313A LYS 3.5 3.9 - - - +
315A ALA* 1.3 92.1 - - + +
317A PRO* 1.2 62.6 - - - +
319A LEU* 3.0 13.0 + - + -
320A TYR* 3.2 39.6 + + + +
331A TRP* 3.9 18.8 - + - -
634C GLU* 3.5 22.2 - - + -
635C LEU* 2.9 49.6 - - + -
638C ASP* 2.9 25.9 - - + +
882C GLY* 6.2 2.9 - - - -
884C GLU* 4.6 13.2 - - + -
885C THR* 4.6 7.4 - - - -
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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