Contacts of the helix formed by residues 362 - 366 (chain B) in PDB entry 4H3I
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 LEU 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B VAL* 3.5 27.1 - - + -
360B THR* 5.5 0.7 - - + -
361B ILE* 1.3 76.0 - - - +
363B PRO* 1.3 70.3 - - + +
364B GLN* 2.9 13.2 - - + +
365B GLN* 2.7 33.2 + - - +
366B TYR* 3.2 16.0 + - - -
421B HIS* 4.8 0.2 - - + -
422B VAL 4.0 5.2 - - - +
423B HIS* 3.6 36.3 - - + -
424B ASP* 4.8 1.1 - - - +
427B ARG* 3.7 31.4 - - + +
428B THR* 3.9 23.1 - - - +
429B ALA* 3.9 2.9 - - - +
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Residues in contact with PRO 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B TRP* 3.6 26.2 - - + +
341B PHE* 3.6 21.1 - - + -
342B PRO 3.8 14.4 - - - +
362B LEU* 1.3 87.8 - - + +
364B GLN* 1.3 64.5 + - - +
366B TYR* 3.5 20.2 - - + -
367B LEU* 2.8 41.1 + - + +
427B ARG* 3.5 27.8 - - - +
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Residues in contact with GLN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLY* 5.7 1.7 - - - -
338B TRP* 3.4 43.6 - - + +
362B LEU* 2.9 17.2 - - + +
363B PRO* 1.3 88.4 - - - +
365B GLN* 1.3 60.8 + - - +
367B LEU 4.0 8.3 - - - +
369B PRO* 5.4 4.3 - - - +
400B GLU* 5.7 0.7 - - - +
422B VAL* 3.4 48.5 - - + +
423B HIS* 3.7 8.3 + - - -
424B ASP* 2.9 44.7 + - - +
427B ARG* 5.0 0.7 + - - -
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ILE* 3.8 18.6 - - + -
362B LEU* 2.7 43.1 + - - +
364B GLN* 1.3 84.1 + - - +
366B TYR* 1.3 61.6 + - - +
367B LEU 3.4 3.8 + - - +
368B ARG* 4.8 2.1 + - - +
384B ALA* 4.9 0.2 - - - +
397B VAL* 3.5 40.4 - - - +
400B GLU* 4.7 13.1 + - + +
401B GLY* 4.1 21.3 - - - +
421B HIS* 4.1 8.6 - - - +
422B VAL* 2.8 39.6 + - - +
429B ALA* 4.4 3.6 - - - +
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Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B ILE* 4.4 4.7 - - + +
341B PHE* 3.4 14.7 - + - +
342B PRO* 2.6 48.2 + - + +
344B ILE* 3.6 27.1 - - + -
361B ILE* 4.2 9.4 - - + -
362B LEU* 3.2 17.4 + - - -
363B PRO* 3.5 20.6 - - + -
365B GLN* 1.3 77.6 - - - +
367B LEU* 1.3 77.3 + - + +
368B ARG 3.7 0.9 - - - -
383B PHE* 3.9 19.7 - + - -
384B ALA* 2.8 34.3 + - - -
385B ILE* 3.9 20.6 - - + -
397B VAL* 3.9 15.7 - - + -
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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