Contacts of the helix formed by residues 314 - 318 (chain A) in PDB entry 5Z66
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 SER 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A TRP* 3.7 12.0 + - - -
313A PHE* 1.3 78.0 - - - +
315A SER* 1.3 63.5 + - - +
316A ARG* 2.9 28.9 + - - +
317A TRP* 3.0 24.2 + - - -
318A MET* 3.2 18.7 - - - +
439A THR* 4.0 2.6 - - - +
445A GLN* 4.2 1.1 - - - +
447A TRP* 2.7 30.1 + - - -
448A ASP* 3.5 8.8 + - - -
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 1.3 72.0 + - - +
316A ARG* 1.3 61.3 + - - +
318A MET* 3.0 34.8 + - - +
321A PRO* 3.8 24.0 - - - -
398A ARG* 4.8 1.0 + - - -
400A GLN* 3.1 25.1 + - - +
441A VAL* 3.6 13.0 - - - +
443A SER* 4.5 0.2 - - - -
448A ASP* 2.7 35.6 + - - -
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Residues in contact with ARG 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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311A TRP* 3.4 40.3 - - - +
314A SER* 2.9 18.7 + - - +
315A SER* 1.3 79.9 + - - +
317A TRP* 1.3 81.6 + - + +
332A ILE* 3.5 6.6 - - - +
334A PRO* 3.6 5.9 - - - +
335A VAL 3.8 1.2 - - - +
336A ASP* 2.8 43.6 + - - -
389A ASP* 2.8 41.6 + - - +
398A ARG* 3.2 23.1 + - - +
400A GLN* 3.4 14.1 - - - +
402A THR* 4.1 21.1 + - + -
404A ALA* 3.5 12.9 - - - +
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Residues in contact with TRP 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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269A TYR* 4.7 1.1 - + - -
306A ALA* 3.9 13.0 - - + +
309A SER* 3.3 31.6 + - - -
311A TRP* 3.0 35.3 + - + +
314A SER* 3.0 18.2 + - - +
316A ARG* 1.3 125.5 - - + +
318A MET* 1.3 61.0 + - - +
327A ILE* 3.6 18.6 - - + -
328A ARG* 2.9 35.2 + - - +
329A THR* 3.7 24.2 - - + +
332A ILE* 3.8 40.2 - - + -
334A PRO* 4.1 16.2 - - + -
389A ASP* 4.2 0.2 - - - -
398A ARG* 5.0 0.7 - - - -
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Residues in contact with MET 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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314A SER 3.2 29.6 - - - +
315A SER* 3.0 21.2 + - - +
316A ARG 3.5 0.2 - - - -
317A TRP* 1.3 81.0 - - - +
319A ASP* 1.3 65.4 + - - +
320A ASP* 3.5 20.8 + - - +
321A PRO* 3.3 27.0 - - + +
322A GLN 4.5 0.4 - - - -
323A LYS 3.5 21.3 - - - +
324A LEU* 3.6 23.1 - - + +
326A THR* 3.9 7.6 - - - +
327A ILE* 4.1 17.5 - - + +
398A ARG* 4.7 7.3 + - - -
445A GLN* 4.2 13.7 - - - +
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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