Contacts of the helix formed by residues 374 - 377 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ARG* 6.0 0.4 - - - +
331A SER* 4.0 20.0 - - - +
332A SER* 4.0 15.3 - - - -
353A GLN 3.3 26.2 - - - +
354A GLU* 3.0 24.4 + - - +
373A ASP* 1.3 76.0 - - - +
375A GLY* 1.3 56.6 + - - +
376A TRP 3.0 4.9 + - - -
377A GLY 3.3 8.5 + - - -
378A LEU* 3.9 20.4 - - + -
635A SER 5.1 0.4 - - - -
636A SER* 3.6 29.6 - - - +
637A ILE* 3.4 19.4 - - + +
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Residues in contact with GLY 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 3.5 27.5 - - - +
143A ILE 5.2 0.5 + - - -
354A GLU* 4.7 0.6 + - - -
372A LEU* 3.1 12.1 + - - +
373A ASP 3.0 1.2 - - - -
374A VAL* 1.3 77.8 - - - +
376A TRP* 1.3 66.2 + - - +
377A GLY 3.7 0.2 - - - -
404A TYR* 3.6 1.5 + - - -
636A SER 4.3 2.2 + - - -
637A ILE* 3.5 22.4 - - - +
640A GLN* 4.1 14.5 - - - +
641A ASN* 5.7 0.5 + - - -
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Residues in contact with TRP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.4 16.8 - - + -
148A TYR* 3.0 26.0 - + - -
186A ASP* 3.6 4.0 - - - -
188A ALA* 4.3 8.7 - - + -
190A ARG* 3.3 29.6 - - - -
371A TYR* 4.4 4.5 - + - -
372A LEU 3.2 16.6 + - - -
373A ASP 2.9 9.2 + - - +
375A GLY* 1.3 82.7 - - - +
377A GLY* 1.3 62.4 + - - +
380A SER* 4.0 2.1 + - - -
381A VAL* 4.6 7.6 - - - +
404A TYR* 3.2 19.2 + - - -
458A VAL* 3.6 20.1 - - + +
640A GLN* 3.0 30.1 + - + +
901A BRN 3.1 53.5 + + - -
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Residues in contact with GLY 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A SER 3.7 8.5 - - - -
331A SER* 3.9 5.4 - - - -
374A VAL 3.3 7.3 + - - -
376A TRP* 1.3 79.3 - - - +
378A LEU* 1.3 58.4 + - - +
379A GLY 3.1 2.9 - - - -
380A SER* 2.7 38.8 + - - -
381A VAL* 3.4 8.9 + - - +
404A TYR* 3.4 20.2 + - - -
458A VAL* 5.2 0.2 - - - -
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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