Contacts of the helix formed by residues 374 - 381 (chain B) in PDB entry 3HIG
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 VAL 374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B SER* 3.9 19.1 - - - +
332B SER* 4.0 20.4 - - - -
353B GLN 3.2 26.7 - - - +
354B GLU* 2.8 34.8 + - - +
373B ASP* 1.3 72.5 - - - +
375B GLY* 1.3 56.1 + - - +
376B TRP 3.1 4.3 + - - -
377B GLY 3.4 8.3 + - - -
378B LEU* 4.1 9.6 - - + -
635B SER* 5.0 0.4 - - - -
636B SER* 3.6 29.6 - - - +
637B ILE* 3.4 18.8 - - + +
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Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO* 3.6 27.1 - - - +
143B ILE 5.1 0.5 + - - -
354B GLU* 4.6 1.0 + - - -
372B LEU* 3.1 11.7 + - - +
373B ASP 3.1 1.6 - - - -
374B VAL* 1.3 76.7 - - - +
376B TRP* 1.3 66.3 + - - +
377B GLY 3.7 0.7 - - - -
404B TYR* 4.2 1.6 - - - -
636B SER 4.3 2.0 + - - -
637B ILE* 3.4 24.2 - - - +
640B GLN* 4.0 14.5 - - - +
641B ASN* 5.8 0.3 + - - -
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Residues in contact with TRP 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 3.3 16.6 - - + -
148B TYR* 3.1 25.8 - + - -
186B ASP* 3.5 4.9 - - - -
188B ALA* 4.3 8.3 - - + -
190B ARG* 3.3 31.0 - - - -
371B TYR* 4.5 4.3 - + - -
372B LEU 3.2 17.5 - - - -
373B ASP* 2.9 9.2 + - - +
375B GLY* 1.3 84.3 - - - +
377B GLY* 1.3 65.2 + - - +
380B SER* 4.2 2.1 + - - -
381B VAL* 4.6 7.8 - - - +
404B TYR* 3.3 16.2 + - - -
458B VAL* 3.7 20.1 - - + +
640B GLN* 2.9 29.3 + - + +
901B BRN 3.3 54.0 + + - -
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Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B SER 3.8 7.9 - - - -
331B SER* 3.9 5.2 - - - -
374B VAL 3.4 6.6 + - - -
376B TRP* 1.3 79.7 - - - +
378B LEU* 1.3 60.3 + - - +
379B GLY 3.2 3.1 - - - -
380B SER* 2.8 30.5 + - - -
381B VAL* 3.5 8.4 + - - +
404B TYR* 3.3 26.1 + - - -
458B VAL* 5.5 0.2 - - - -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B SER 3.1 12.1 + - - +
332B SER 4.1 16.4 - - - +
333B GLY* 4.7 2.8 - - - +
352B VAL* 4.1 14.4 - - + -
355B ALA* 4.0 24.2 - - + +
373B ASP* 3.4 35.9 + - + +
374B VAL* 4.1 16.2 - - + -
377B GLY* 1.3 73.7 - - - +
379B GLY* 1.3 58.4 + - - +
381B VAL* 3.5 8.1 + - - +
455B THR 4.7 2.1 - - - +
456B SER* 3.1 53.9 - - - +
458B VAL* 4.7 4.3 - - + -
463B TYR* 5.0 0.2 - - + -
465B TRP* 4.4 10.8 - - + +
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Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.9 4.3 - - - +
329B ARG 3.3 14.6 - - - -
330B SER* 3.1 16.2 + - - -
331B SER 3.6 3.2 + - - -
333B GLY* 3.7 13.0 - - - +
378B LEU* 1.3 76.9 - - - +
380B SER* 1.3 57.1 + - - +
381B VAL 3.5 0.7 - - - -
382B THR* 3.3 14.9 - - - +
402B HIS* 2.8 24.9 + - - -
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Residues in contact with SER 380 (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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330B SER* 3.0 10.0 + - - -
376B TRP 4.2 0.7 + - - -
377B GLY* 2.8 21.4 + - - -
379B GLY* 1.3 77.2 - - - +
381B VAL* 1.3 64.9 + - - +
382B THR 3.3 5.4 - - - -
402B HIS* 3.6 17.8 - - - -
404B TYR* 3.7 36.4 - - - -
412B TYR* 3.4 31.4 + - - -
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TRP 4.6 6.3 - - - +
377B GLY 3.5 7.9 - - - +
378B LEU 3.5 16.6 - - - +
379B GLY 3.5 0.2 - - - -
380B SER* 1.3 87.4 - - - +
382B THR* 1.3 57.5 + - - +
383B HIS* 3.1 28.5 + - + +
412B TYR* 5.8 0.4 - - - +
455B THR* 4.2 1.6 + - - -
456B SER* 3.5 6.8 - - - -
457B THR 3.1 52.9 + - - +
458B VAL* 3.9 20.4 - - + +
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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