Contacts of the helix formed by residues 356 - 360 (chain D) in PDB entry 2QJK
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 356 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D TYR* 3.8 15.0 - - - -
224D PRO 2.9 18.5 + - - -
225D THR 3.4 32.0 + - - -
226D GLY* 3.7 3.8 - - - -
354D VAL* 3.7 17.1 - - - +
355D ARG* 1.3 81.5 - - - +
357D GLY* 1.3 60.4 + - - +
358D ARG* 3.0 20.3 + - - +
359D TYR* 3.5 14.7 + - - +
360D ARG* 3.9 2.1 - - - +
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Residues in contact with GLY 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D TYR* 3.0 33.8 + - - -
355D ARG 3.4 2.4 + - - -
356D SER* 1.3 70.4 + - - +
358D ARG* 1.3 60.0 + - - +
359D TYR 2.9 7.0 + - - -
360D ARG* 3.3 26.6 + - - +
363D PHE* 4.4 11.6 - - - -
364D LYS* 3.6 18.2 - - - +
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Residues in contact with ARG 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ASN* 4.4 4.0 - - - +
117D TYR* 3.5 16.3 + - + +
118D TYR* 4.2 3.2 + - - -
224D PRO* 3.1 43.5 + - - +
225D THR* 4.0 0.8 - - - +
356D SER* 3.0 15.0 + - - +
357D GLY* 1.3 78.4 - - - +
359D TYR* 1.3 87.6 + - + +
360D ARG 3.5 0.2 - - - -
364D LYS* 2.8 27.5 + - - +
418D VAL* 5.6 0.5 - - - +
427D ASP* 3.5 24.7 + - - -
503D LOP 3.0 52.3 + - - +
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Residues in contact with TYR 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D THR* 3.4 38.9 - - - +
354D VAL* 4.3 8.2 - - + +
356D SER* 3.5 17.1 + - - +
357D GLY 2.9 0.8 - - - -
358D ARG* 1.3 117.8 + - + +
360D ARG* 1.3 62.8 + - - +
361D PRO* 3.8 4.7 - - - -
364D LYS* 4.8 0.2 - - - +
417D PRO* 3.6 6.9 - - - +
418D VAL* 3.1 48.0 + - + +
419D ALA 4.5 8.1 - - - -
420D PRO* 3.6 25.8 - - + -
421D PRO* 3.2 27.5 - - + +
427D ASP* 4.0 1.7 + - - -
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Residues in contact with ARG 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D TYR* 4.9 0.4 + - - -
122D LYS* 3.1 14.3 - - - +
350D ASP* 3.1 28.3 + - - -
352D SER* 3.2 28.5 + - - +
354D VAL* 4.0 22.6 + - + -
355D ARG 5.0 1.6 + - - -
356D SER 3.9 13.2 - - - +
357D GLY* 3.3 13.3 + - - +
358D ARG 3.5 1.4 + - - -
359D TYR* 1.3 84.5 - - - +
361D PRO* 1.3 58.5 - - - +
363D PHE* 3.1 38.5 + - + -
364D LYS* 2.9 36.6 + - - +
408D LEU* 4.4 4.0 + - - +
411D LEU* 4.2 15.4 - - - +
412D GLY 4.8 0.4 - - - +
415D GLU* 3.1 26.3 + - + +
417D PRO* 5.2 0.9 - - + -
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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