Contacts of the helix formed by residues 705 - 716 (chain B) in PDB entry 5J3V
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 CYS 705 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669B LEU* 4.2 31.9 - - + -
701B HIS 4.4 3.6 - - - +
702B VAL* 2.8 9.5 + - - +
704B PRO* 1.3 80.1 - - - +
706B ILE* 1.3 62.8 + - - +
707B ALA 3.3 2.5 - - - -
708B ASP* 3.4 16.5 + - + +
709B PHE* 3.1 47.8 + - + -
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Residues in contact with ILE 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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699B PHE* 3.8 17.5 - - + -
702B VAL* 4.0 15.5 - - + -
703B LYS* 3.2 31.2 + - - +
704B PRO 3.3 0.4 - - - -
705B CYS* 1.3 74.0 - - - +
707B ALA* 1.3 66.2 + - - +
708B ASP 3.1 2.0 - - - -
709B PHE* 4.4 6.1 - - + +
710B MET* 3.0 42.7 + - + +
735B ILE* 3.7 34.5 - - + -
739B MET* 4.3 13.0 - - + -
743B MET* 5.8 0.4 - - + -
746B TYR* 4.0 23.6 - - + +
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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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703B LYS 4.8 0.4 + - - -
704B PRO 4.4 8.4 + - - +
705B CYS 3.3 0.6 - - - -
706B ILE* 1.3 78.3 - - - +
708B ASP* 1.3 66.9 + - - +
711B PRO* 3.3 20.5 - - - +
746B TYR* 4.4 21.0 + - + +
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Residues in contact with ASP 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B TYR* 4.0 35.7 + - + +
704B PRO 5.4 1.2 - - - +
705B CYS* 3.4 16.6 + - + +
706B ILE 3.1 0.4 - - - -
707B ALA* 1.3 89.7 - - - +
709B PHE* 1.3 68.0 + - + +
710B MET 3.5 0.2 - - - -
711B PRO* 3.3 12.0 - - - +
712B ILE* 3.5 19.6 - - - +
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Residues in contact with PHE 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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669B LEU* 3.8 32.3 - - + -
672B MET* 5.1 2.5 - - + -
673B TYR* 4.0 27.1 - + + -
676B MET* 3.6 31.7 - - + +
691B LEU* 3.6 39.5 - - + -
702B VAL* 4.4 8.3 - - + -
705B CYS* 3.1 39.3 + - + +
706B ILE* 3.2 9.2 + - + +
708B ASP* 1.3 81.3 - - + +
710B MET* 1.3 59.1 + - - +
712B ILE* 3.1 7.7 + - - +
713B LEU* 2.8 34.2 + - + +
735B ILE* 5.6 0.2 - - + -
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Residues in contact with MET 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B ILE* 3.0 36.1 + - + +
709B PHE* 1.3 76.7 - - - +
711B PRO* 1.3 68.8 - - + +
713B LEU* 3.3 22.5 + - + +
714B GLY* 3.0 19.1 + - - -
732B ILE* 4.6 14.6 - - + -
735B ILE* 4.4 12.8 - - - -
743B MET* 4.7 11.2 - - - +
746B TYR* 3.7 40.6 - - + +
749B MET* 4.2 8.7 - - + +
750B VAL* 3.7 31.5 - - + +
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Residues in contact with PRO 711 (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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707B ALA 3.3 25.8 - - - +
708B ASP* 3.3 11.2 - - - +
710B MET* 1.3 93.3 - - + +
712B ILE* 1.3 57.8 + - + +
714B GLY* 3.4 2.0 + - - -
715B THR* 3.1 33.2 + - + +
746B TYR* 5.8 0.7 - - + -
749B MET* 4.3 16.6 - - + -
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Residues in contact with ILE 712 (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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673B TYR* 3.4 37.0 - - + +
676B MET* 3.8 32.5 - - + +
677B GLN* 3.9 20.6 - - + -
688B PHE* 4.0 4.7 - - + -
708B ASP 3.5 11.7 - - - +
709B PHE* 3.1 8.6 + - - +
711B PRO* 1.3 75.8 - - + +
713B LEU* 1.3 65.2 + - - +
714B GLY 3.1 0.2 - - - -
715B THR* 2.8 12.3 + - - +
716B ASN* 2.4 41.3 + - - +
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Residues in contact with LEU 713 (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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676B MET* 5.9 0.2 - - - -
688B PHE* 3.6 34.1 - - + -
691B LEU* 4.0 15.3 - - + -
709B PHE 2.8 22.8 + - - +
710B MET* 3.3 20.2 + - + +
712B ILE* 1.3 77.1 - - - +
714B GLY* 1.3 60.7 + - - +
716B ASN* 3.4 8.0 + - - +
717B LEU* 3.3 23.7 + - - +
728B ALA* 4.0 21.6 - - - +
731B ALA* 4.1 4.7 - - + -
732B ILE* 3.9 22.7 - - + +
735B ILE* 3.8 29.6 - - + -
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Residues in contact with GLY 714 (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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710B MET 3.0 13.5 + - - -
711B PRO 3.8 3.8 - - - -
712B ILE 3.1 0.2 - - - -
713B LEU* 1.3 74.6 - - - +
715B THR* 1.3 59.6 + - - +
716B ASN 3.1 5.8 + - - -
717B LEU* 3.4 11.7 + - - +
718B ASN* 5.2 0.2 - - - +
749B MET* 3.9 10.1 - - - -
750B VAL* 4.3 3.1 - - - +
753B GLN* 2.8 40.9 + - - +
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Residues in contact with THR 715 (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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711B PRO* 3.1 13.4 + - + +
712B ILE* 2.8 26.9 + - - +
714B GLY* 1.3 76.1 - - - +
716B ASN* 1.3 63.7 + - - +
717B LEU 3.4 1.8 - - - -
718B ASN* 3.2 18.0 - - - +
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Residues in contact with ASN 716 (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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676B MET 4.4 3.0 + - - -
684B ARG* 3.1 39.5 + - - +
688B PHE* 3.5 25.7 - - + -
712B ILE* 2.4 43.4 + - - +
713B LEU 3.4 7.8 + - - +
714B GLY 3.1 0.8 - - - -
715B THR* 1.3 89.7 + - - +
717B LEU* 1.3 56.1 + - - +
718B ASN* 3.1 10.7 + - - +
724B VAL* 4.3 4.5 - - + +
725B CYS* 3.6 20.8 + - - +
728B ALA* 3.6 4.7 - - + +
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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