Contacts of the helix formed by residues 699 - 710 (chain B) in PDB entry 4OSI
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 THR 699 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698B LEU* 1.3 84.6 - - + +
700B ASN* 1.3 60.7 + - - +
701B ASP* 3.7 15.1 + - - +
702B HIS* 2.9 52.9 + - + +
703B LEU* 3.2 7.3 - - - +
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Residues in contact with ASN 700 (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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661B HIS* 3.5 24.0 + - - +
662B GLY 5.3 4.9 - - - +
663B LEU* 5.5 5.8 - - + +
688B LEU* 3.1 38.6 - - + +
698B LEU 3.7 8.3 - - - +
699B THR* 1.3 71.8 + - - +
701B ASP* 1.3 61.6 + - - +
702B HIS 2.6 15.8 + - - -
703B LEU* 2.6 26.9 + - + +
704B VAL* 2.9 12.8 + - + +
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Residues in contact with ASP 701 (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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662B GLY 4.9 5.9 - - - +
663B LEU* 5.9 0.2 - - - -
667B GLN* 3.5 26.7 + - - +
699B THR* 3.7 9.1 + - - +
700B ASN* 1.3 77.9 + - - +
702B HIS* 1.3 63.7 + - - +
704B VAL* 3.0 15.5 - - + +
705B ALA* 2.9 20.6 + - - +
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Residues in contact with HIS 702 (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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698B LEU* 2.9 38.9 - - + +
699B THR* 2.9 33.6 + - + +
700B ASN 2.6 2.4 + - - -
701B ASP* 1.3 68.9 - - - +
703B LEU* 1.3 60.2 + - + +
704B VAL 2.4 16.9 + - - -
705B ALA* 2.7 20.1 + - + +
706B LEU* 2.9 26.8 + - + +
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Residues in contact with LEU 703 (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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684B ILE* 3.5 25.4 - - + +
687B GLN* 4.5 19.3 - - - +
688B LEU* 4.1 20.4 - - + -
691B PRO* 6.2 0.7 - - + -
697B ALA* 6.0 1.1 - - + -
698B LEU* 4.0 24.0 - - + +
699B THR 3.2 20.4 - - - +
700B ASN* 2.6 19.5 + - - +
702B HIS* 1.3 74.9 - - + +
704B VAL* 1.3 63.8 + - - +
706B LEU* 3.2 23.7 - - + +
707B ALA* 2.9 23.4 + - - +
715B LEU* 4.9 5.1 - - + +
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Residues in contact with VAL 704 (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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663B LEU* 4.3 16.6 - - + -
667B GLN* 3.5 43.3 - - + +
671B ILE* 4.8 16.8 - - + -
684B ILE* 5.4 2.5 - - + -
700B ASN* 2.9 8.1 + - + +
701B ASP* 3.0 24.2 - - + +
702B HIS 2.4 11.1 + - - -
703B LEU* 1.3 68.5 - - - +
705B ALA* 1.3 73.8 + - + +
706B LEU 2.6 2.9 + - - -
707B ALA* 3.5 0.7 - - - +
708B CYS* 2.9 32.0 + - - -
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Residues in contact with ALA 705 (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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701B ASP 2.9 7.5 + - - +
702B HIS* 2.7 12.0 + - + +
704B VAL* 1.3 78.4 - - + +
706B LEU* 1.3 63.8 + - - +
708B CYS* 3.2 11.2 - - - +
709B LEU* 2.9 21.5 + - - +
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Residues in contact with LEU 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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698B LEU* 6.1 1.1 - - + -
702B HIS* 2.9 25.6 + - + +
703B LEU* 3.2 31.9 - - + +
704B VAL 2.6 3.2 + - - -
705B ALA* 1.3 67.8 - - - +
707B ALA* 1.3 55.7 + - - +
708B CYS 2.5 17.0 + - - -
709B LEU* 2.5 20.4 + - + +
710B GLY* 2.9 9.8 + - - -
711B GLY 4.4 1.3 - - - -
714B ALA* 3.9 22.7 - - + -
715B LEU* 3.4 22.7 - - + -
718B VAL* 4.0 25.6 - - + -
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Residues in contact with ALA 707 (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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671B ILE* 4.2 27.9 - - + +
674B ASN* 4.7 0.9 - - - +
680B ALA* 4.4 20.0 - - + +
684B ILE* 4.3 13.0 - - + -
703B LEU 2.9 15.9 + - - +
704B VAL 3.7 2.2 - - - +
706B LEU* 1.3 76.4 - - - +
708B CYS* 1.3 61.0 + - - +
711B GLY* 2.9 30.8 + - - +
715B LEU* 4.0 7.7 - - + +
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Residues in contact with CYS 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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670B ALA* 3.3 38.8 - - - +
671B ILE* 4.0 6.3 - - - +
674B ASN* 2.7 33.5 + - - +
704B VAL* 2.9 29.5 + - - -
705B ALA* 3.2 13.9 - - - +
706B LEU 2.5 6.9 + - - -
707B ALA* 1.3 74.6 - - - +
709B LEU* 1.3 60.7 + - + +
710B GLY 5.2 0.2 - - - -
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Residues in contact with LEU 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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674B ASN* 5.9 0.9 - - - +
705B ALA 2.9 14.5 + - - +
706B LEU* 2.5 10.4 + - - +
708B CYS* 1.3 75.1 - - - +
710B GLY* 1.3 54.4 + - - +
16G C 6.2 0.5 - - - -
17G T 4.9 14.3 - - + +
-1H A 6.3 0.9 - - - +
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Residues in contact with GLY 710 (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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706B LEU 2.9 9.5 + - - -
707B ALA 3.9 0.2 - - - -
708B CYS 3.3 0.8 - - - -
709B LEU* 1.3 80.2 - - - +
711B GLY* 1.3 65.5 + - - +
713B PRO* 3.0 24.4 - - - +
714B ALA* 4.1 15.9 - - - -
16G C 5.9 2.0 - - - -
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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