Contacts of the helix formed by residues 536 - 540 (chain A) in PDB entry 3V9G
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 HIS 536 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A ASP 4.6 3.6 - - - +
531A LYS* 6.1 2.9 - - + -
534A GLY* 3.3 1.0 - - - -
535A PRO* 1.3 93.1 - - + +
537A TYR* 1.3 66.8 + - - +
538A ILE 3.3 2.5 - - - -
539A LEU* 3.0 30.4 + - + +
540A ARG* 4.2 2.6 + - - +
180B LEU* 3.6 24.6 - - + +
183B GLN* 3.2 35.1 + - + -
197B TYR* 3.7 22.0 + + - -
536B HIS* 5.8 1.8 - + - -
539B LEU* 3.8 31.7 - - + +
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Residues in contact with TYR 537 (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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173A ASN* 4.6 7.4 - - - +
218A ASN* 3.5 26.2 + - - -
219A LEU* 4.2 5.7 - - - +
222A ALA* 3.6 25.8 - - + -
283A ASN* 3.0 33.8 + - - -
312A ALA* 5.5 2.2 - - + -
530A ASP* 3.5 29.3 + - + -
531A LYS 3.6 16.9 + - - +
532A PRO* 3.6 36.1 - - + +
533A GLY 4.7 0.4 - - - +
534A GLY 3.7 9.7 + - - +
535A PRO 3.6 0.4 - - - -
536A HIS* 1.3 78.3 - - - +
538A ILE* 1.3 69.7 + - + +
539A LEU 3.1 0.9 + - - -
540A ARG* 3.2 21.3 + - + +
541A TRP* 3.7 17.3 - + - -
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Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASN* 3.9 36.6 - - + +
176A TYR* 3.7 15.9 - - + +
177A ALA* 3.7 33.0 - - - +
180A LEU* 4.2 11.2 - - + -
222A ALA* 4.8 5.8 - - + -
225A LEU* 4.8 2.2 - - + -
226A MET* 3.9 32.8 - - + +
534A GLY 5.5 0.2 - - - +
535A PRO 3.7 17.5 - - - +
537A TYR* 1.3 78.1 - - + +
539A LEU* 1.3 59.1 + - + +
541A TRP* 2.9 31.7 + - - +
542A THR* 3.8 6.7 + - - +
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Residues in contact with LEU 539 (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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180A LEU* 3.8 37.9 - - + -
197A TYR* 5.2 1.3 - - + -
310A ARG* 3.5 3.6 + - - -
535A PRO 4.9 2.9 - - - +
536A HIS* 3.0 27.4 + - + +
538A ILE* 1.3 79.1 - - + +
540A ARG* 1.3 64.8 + - + +
541A TRP 3.1 0.7 + - - -
542A THR* 3.3 26.9 + - + +
536B HIS* 3.7 28.9 - - + +
539B LEU* 3.3 34.8 - - + -
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Residues in contact with ARG 540 (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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200A LEU* 4.1 0.7 - - - +
310A ARG* 2.8 81.3 + - + +
311A LEU 4.7 10.1 + - - +
312A ALA* 5.7 2.3 - - + +
530A ASP* 3.7 38.3 + - + +
536A HIS 5.1 2.5 - - - +
537A TYR* 3.2 14.7 + - + +
538A ILE 3.1 0.8 - - - -
539A LEU* 1.3 79.9 + - - +
541A TRP* 1.3 82.6 + - + +
530B ASP* 4.6 4.9 + - - -
540B ARG* 3.9 45.3 - - - +
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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