Contacts of the helix formed by residues 283 - 287 (chain A) in PDB entry 5C16
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 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A VAL* 3.5 16.2 - - + +
280A ALA 2.9 10.6 + - - +
281A ALA 4.6 0.2 - - - -
282A PHE* 1.3 82.7 + - - +
284A ALA* 1.3 66.4 + - - +
285A LYS 3.2 0.9 + - - -
286A GLY 2.9 13.9 + - - -
287A ARG 3.8 20.0 - - - +
288A VAL* 4.3 9.6 - - - +
289A PRO* 4.4 8.2 - - - +
305A CYS* 3.6 14.4 - - - -
306A SER* 3.0 34.4 + - - +
307A GLN 3.7 3.8 - - - -
308A PRO* 3.4 17.9 - - - +
309A LEU* 3.9 7.0 - - - +
320A ASP* 2.8 37.2 + - - +
324A LEU* 4.1 14.6 - - - +
359A GLU* 2.7 37.5 + - - +
437A HIS* 3.9 1.0 - - - -
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Residues in contact with ALA 284 (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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283A ARG* 1.3 69.0 - - - +
285A LYS* 1.3 64.6 + - + +
286A GLY 2.9 5.7 + - - -
287A ARG* 3.1 5.0 + - - +
306A SER* 2.7 28.8 + - - +
307A GLN* 3.2 18.9 + - + +
309A LEU* 3.8 15.3 - - + +
439A SER 4.1 13.5 - - - +
440A ASP* 4.1 11.7 - - - +
580B TYR* 4.1 24.9 - - + -
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A CYS* 3.3 17.8 - - - +
259A ASP* 5.1 3.7 + - - +
260A THR* 4.4 7.9 + - + +
283A ARG 3.2 1.2 + - - -
284A ALA* 1.3 74.5 - - + +
286A GLY* 1.3 62.7 + - - +
287A ARG* 3.1 16.6 + - + -
440A ASP* 2.8 39.1 + - - +
442A TRP* 3.7 27.4 - - + -
578B VAL* 6.4 0.2 - - - +
579B ASN* 5.8 3.2 - - - +
580B TYR* 4.8 14.5 + - - -
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PHE* 4.2 3.9 - - - -
258A CYS* 3.5 19.0 - - - +
280A ALA* 3.3 31.7 + - - +
283A ARG* 2.9 8.1 + - - -
285A LYS* 1.3 76.8 - - - +
287A ARG* 1.3 59.4 + - - +
288A VAL* 3.0 18.2 + - - +
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A CYS* 3.7 7.9 - - - -
260A THR* 2.9 42.6 + - - +
261A TYR* 3.3 32.8 - - - +
283A ARG* 3.8 5.3 + - - +
284A ALA 3.1 7.4 + - - +
285A LYS* 3.6 23.6 - - - +
286A GLY* 1.3 74.3 - - - +
288A VAL* 1.3 64.1 + - - +
304A ARG* 3.6 9.7 - - - +
305A CYS* 3.3 2.3 - - - +
306A SER* 3.2 33.5 + - - +
440A ASP 3.0 25.4 + - - -
441A GLY* 3.0 20.9 + - - -
442A TRP* 3.6 19.7 - - - +
477A PHE 2.8 29.3 + - - -
478A GLY* 4.6 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