Contacts of the helix formed by residues 337 - 341 (chain B) in PDB entry 4H3J
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 PRO 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B GLU* 3.6 25.4 - - - +
331B TRP* 3.3 36.6 - - + +
335B THR 3.4 9.0 - - - +
336B THR* 1.3 82.8 - - + +
338B TRP* 1.3 65.1 + - - +
339B ASN* 3.1 12.6 - - - +
340B ILE* 3.0 37.3 + - + +
341B PHE* 3.6 5.9 - - + -
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Residues in contact with TRP 338 (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 5.6 3.4 - - - -
336B THR* 2.9 39.2 + - + +
337B PRO* 1.3 70.5 - - - +
339B ASN* 1.3 57.7 + - - +
341B PHE* 3.0 22.5 + - - +
363B PRO* 3.6 33.8 - - + +
364B GLN* 3.3 47.3 - - + +
367B LEU* 4.0 16.2 - - + -
381B TYR* 3.4 43.7 - + - -
422B VAL* 6.1 0.9 - - + -
424B ASP* 3.7 23.6 - - + +
427B ARG* 2.9 17.8 + - - +
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Residues in contact with ASN 339 (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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270B ASN* 5.8 1.0 + - - -
337B PRO* 3.0 16.0 + - - +
338B TRP* 1.3 78.9 - - - +
340B ILE* 1.3 74.7 + - - +
341B PHE 3.2 5.7 + - - +
424B ASP* 5.2 0.8 + - - -
426B PHE* 6.0 6.3 - - + -
427B ARG* 4.0 14.5 + - - +
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Residues in contact with ILE 340 (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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270B ASN* 5.8 0.3 + - - -
312B ALA* 3.2 23.8 - - - +
313B SER* 3.3 18.7 - - - +
315B THR* 3.7 22.2 - - + +
316B GLU* 3.7 43.3 - - + +
318B PHE* 4.5 2.0 - - + -
337B PRO* 3.0 31.1 + - + +
339B ASN* 1.3 92.0 - - - +
341B PHE* 1.3 75.3 + - + +
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Residues in contact with PHE 341 (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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270B ASN* 4.8 1.7 + - - -
309B ILE* 4.7 3.4 - - + -
313B SER* 4.2 13.7 - - - -
318B PHE* 3.6 33.4 - + - -
322B PHE* 4.6 7.2 - + - -
323B TRP* 4.4 13.0 - + - -
331B TRP* 4.0 22.4 - + - -
336B THR* 5.8 1.1 - - + -
337B PRO* 3.6 17.5 - - + -
338B TRP* 3.0 9.5 + - - +
339B ASN 3.9 0.9 - - - +
340B ILE* 1.3 92.4 - - + +
342B PRO* 1.3 65.6 - - + +
363B PRO* 3.5 13.0 - - + -
366B TYR* 3.4 24.9 - + - +
367B LEU* 4.1 25.6 - - + -
427B ARG* 2.9 29.9 + - - -
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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