Contacts of the helix formed by residues 678 - 682 (chain B) in PDB entry 3HI7
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 678 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A TYR* 5.3 2.2 + + - -
594A ARG* 5.7 2.4 + - - -
697A ARG* 4.6 20.7 + - + -
698A PRO 3.5 17.6 + - - -
699A PHE* 3.5 27.7 - + + -
700A ASN* 3.3 15.7 - - - +
501B LEU* 3.3 11.7 - - - +
675B HIS* 4.8 5.2 + + - -
676B ILE 3.4 15.5 - - - -
677B PRO* 1.3 74.8 - - - +
679B SER* 1.3 61.6 + - - +
680B GLU* 2.8 34.0 + - + +
681B ASP* 2.8 48.0 + - - +
690B ASN* 5.8 0.4 + - - -
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Residues in contact with SER 679 (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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585A ASN* 3.2 24.5 + - - -
587A TRP* 3.9 10.3 - - - -
700A ASN* 2.9 16.6 + - - -
702A PHE 2.5 26.7 + - - -
703A PRO 3.5 13.7 - - - -
704A GLU* 3.2 15.7 - - - -
500B ARG 5.3 0.2 - - - -
501B LEU* 3.6 10.6 - - - +
678B HIS* 1.3 72.0 - - - +
680B GLU* 1.3 59.9 + - - +
681B ASP 3.1 0.2 - - - -
682B ILE* 3.2 19.0 + - - +
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Residues in contact with GLU 680 (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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698A PRO* 3.4 29.3 - - + +
700A ASN 2.9 17.9 + - - -
701A PHE 2.8 25.7 + - - -
702A PHE* 2.9 17.9 + - + -
705A ASP* 3.3 27.8 - - - +
706A PRO* 3.8 25.4 - - + -
678B HIS* 2.8 29.2 + - + +
679B SER* 1.3 79.3 - - - +
681B ASP* 1.3 55.9 + - - +
682B ILE 3.1 5.1 + - - -
684B ASN 3.8 4.0 - - - +
686B ALA* 5.7 1.7 + - - +
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Residues in contact with ASP 681 (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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212B LEU* 6.1 0.2 - - - +
485B VAL* 4.2 16.8 + - + +
501B LEU* 4.9 6.7 - - + -
675B HIS* 2.8 29.7 + - - -
677B PRO* 3.3 3.6 - - - +
678B HIS* 2.8 47.2 + - - +
680B GLU* 1.3 74.8 - - - +
682B ILE* 1.3 61.2 + - - +
683B PRO 3.2 4.2 - - - +
684B ASN* 3.0 27.6 + - - -
685B THR* 3.3 25.9 + - - +
686B ALA 4.7 1.0 + - - -
690B ASN* 5.0 2.3 + - - -
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Residues in contact with ILE 682 (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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703A PRO 5.3 0.2 - - - +
704A GLU* 3.5 16.2 - - + +
705A ASP* 2.8 31.5 + - - +
212B LEU* 3.8 17.7 - - + -
282B PHE* 3.5 36.3 - - + +
485B VAL* 5.3 1.1 - - + -
501B LEU* 3.9 41.3 - - + +
502B HIS* 5.3 1.8 - - + -
505B LEU* 3.8 28.3 - - + -
679B SER 3.5 13.0 - - - +
680B GLU 3.1 1.6 - - - -
681B ASP* 1.3 81.2 - - - +
683B PRO* 1.4 67.2 - - + +
684B ASN 3.5 0.7 - - - -
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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