Contacts of the helix formed by residues 705 - 710 (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 ASP 705 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A GLU 3.4 20.9 + - - +
682A ILE 2.7 24.6 + - - +
683A PRO* 4.3 2.0 - - + +
684A ASN 4.7 5.1 - - - +
686A ALA* 5.2 4.1 - - - +
427B LEU* 4.6 2.9 - - - +
428B ARG* 2.9 23.6 + - - -
472B ASN* 3.9 7.9 - - - +
704B GLU* 1.3 69.6 - - - +
706B PRO* 1.3 72.1 - - - +
707B SER* 2.8 37.6 + - - -
708B LEU* 3.3 27.1 + - + +
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Residues in contact with PRO 706 (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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291A PHE* 3.6 18.5 - - - -
680A GLU* 3.9 17.0 - - + -
341B PHE* 3.6 21.9 - - + -
471B PRO 4.5 2.7 - - - -
472B ASN* 3.0 32.3 - - + +
702B PHE* 3.6 28.9 - - + -
704B GLU 3.0 8.5 - - - +
705B ASP* 1.3 89.6 - - - +
707B SER* 1.3 54.8 + - - -
708B LEU* 3.1 5.6 + - - -
709B ALA* 3.8 5.5 + - - +
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Residues in contact with SER 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 4.4 4.5 - - - -
427B LEU* 3.8 7.6 - - - +
428B ARG* 2.9 22.2 + - - -
445B LEU* 4.2 11.0 - - - -
471B PRO* 3.9 16.8 + - - -
472B ASN* 3.9 16.2 - - - -
705B ASP* 2.8 30.5 + - - -
706B PRO* 1.3 75.6 - - - +
708B LEU* 1.3 57.5 + - - +
709B ALA 3.1 3.4 - - - -
710B SER* 2.9 24.9 + - - -
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Residues in contact with LEU 708 (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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285A HIS 4.0 17.7 - - - +
286A LYS 4.1 2.0 - - - +
287A PRO* 3.1 13.2 - - - +
288A ARG* 3.0 58.3 + - + +
682A ILE 3.9 2.7 - - - +
683A PRO* 3.6 31.0 - - + -
428B ARG* 3.7 14.4 - - - +
704B GLU* 3.5 31.4 - - - +
705B ASP* 3.3 22.2 - - + +
706B PRO 3.1 1.8 - - - -
707B SER* 1.3 77.2 + - - +
709B ALA* 1.3 60.6 + - - +
710B SER 3.4 1.8 + - - +
713B THR* 5.5 0.2 + - - -
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Residues in contact with ALA 709 (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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288A ARG 3.2 9.8 + - - +
289A GLY* 3.8 18.4 - - - +
290A ASP 3.9 1.6 - - - +
291A PHE* 3.7 45.3 + - + +
706B PRO 3.8 4.7 + - - +
707B SER 3.1 0.4 - - - -
708B LEU* 1.3 76.1 - - - +
710B SER* 1.3 61.0 + - - +
711B ARG* 2.5 29.7 + - - +
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Residues in contact with SER 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO* 3.6 19.1 - - - +
291A PHE* 3.6 19.2 - - - -
445B LEU* 3.6 18.9 - - - +
471B PRO* 5.8 4.3 - - - -
707B SER* 2.9 18.7 + - - -
708B LEU 3.8 1.6 - - - +
709B ALA* 1.3 78.5 - - - +
711B ARG* 1.3 62.5 + - - +
712B ASP* 3.2 27.5 + - - +
713B THR* 3.7 8.2 + - - -
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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