Contacts of the helix formed by residues 703 - 724 (chain B) in PDB entry 5IJO
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 PRO 703 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701B SER 4.1 0.6 - - - -
702B VAL* 1.3 80.3 - - - +
704B CYS* 1.3 60.3 + - - +
705B GLN* 3.3 8.3 - - + +
706B LEU* 3.3 11.0 + - + +
707B LEU* 3.0 25.1 + - - +
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Residues in contact with CYS 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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703B PRO* 1.3 69.5 - - - +
705B GLN* 1.3 66.6 + - - +
707B LEU* 3.0 10.2 + - - +
708B GLU* 2.9 23.8 + - - +
799B CYS* 4.3 23.8 - - + -
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Residues in contact with GLN 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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703B PRO* 3.3 5.8 - - + +
704B CYS* 1.3 79.9 - - - +
706B LEU* 1.3 57.9 + - - +
708B GLU* 3.2 7.2 + - - +
709B SER* 2.9 26.7 + - - -
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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
----------------------------------------------------------
702B VAL* 4.4 10.1 - - + -
703B PRO* 3.3 21.9 + - + +
704B CYS 3.1 0.6 - - - -
705B GLN* 1.3 76.8 - - - +
707B LEU* 1.3 65.3 + - - +
709B SER* 3.0 9.7 + - - -
710B VAL* 2.9 24.1 + - - +
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Residues in contact with LEU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B VAL* 5.3 5.1 - - + +
703B PRO 3.0 12.6 + - - +
704B CYS* 3.0 13.3 + - - +
706B LEU* 1.3 74.5 - - - +
708B GLU* 1.3 58.7 + - - +
710B VAL* 3.3 5.8 + - - +
711B LEU* 2.9 30.9 + - - +
792B LEU* 5.1 5.3 - - + +
795B TRP* 5.2 16.4 - - + +
796B LYS* 5.3 11.7 - - - +
799B CYS* 6.0 2.5 - - + -
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Residues in contact with GLU 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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704B CYS 2.9 12.0 + - - +
705B GLN* 3.5 10.3 - - - +
707B LEU* 1.3 76.6 - - - +
709B SER* 1.3 57.0 + - - +
711B LEU* 3.3 5.9 + - - +
712B GLN* 2.8 32.1 + - - +
796B LYS* 6.2 2.9 - - - -
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Residues in contact with SER 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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705B GLN 2.9 13.5 + - - -
706B LEU* 3.3 12.3 - - - -
708B GLU* 1.3 78.3 - - - +
710B VAL* 1.3 62.2 + - - +
712B GLN* 3.2 5.9 + - - +
713B GLU* 3.0 23.7 + - - +
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Residues in contact with VAL 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B LEU 2.9 14.5 + - - +
707B LEU* 3.8 5.4 - - - +
709B SER* 1.3 75.0 - - - +
711B LEU* 1.3 64.5 + - - +
713B GLU* 3.2 5.9 + - - +
714B LEU* 2.9 26.7 + - - +
792B LEU* 5.3 5.6 - - + -
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Residues in contact with LEU 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 LEU 2.9 18.1 + - - +
708B GLU* 3.6 7.2 - - - +
710B VAL* 1.3 78.5 - - - +
712B GLN* 1.3 55.8 + - - +
714B LEU* 3.4 4.0 + - - +
715B LYS* 2.9 30.2 + - - +
789B TYR* 5.9 2.2 - - - +
792B LEU* 4.1 28.7 - - + +
793B ALA* 5.4 1.6 - - - +
796B LYS* 5.5 6.5 - - + -
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Residues in contact with GLN 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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708B GLU 2.8 18.6 + - - +
709B SER* 3.6 6.1 - - - +
711B LEU* 1.3 76.7 - - - +
713B GLU* 1.3 63.0 + - - +
715B LYS* 3.1 9.0 + - - +
716B GLY* 3.0 18.5 + - - -
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Residues in contact with GLU 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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673B ILE* 6.0 6.7 - - + -
709B SER 3.0 16.3 + - - +
710B VAL* 3.7 6.3 - - - +
712B GLN* 1.3 77.4 - - - +
714B LEU* 1.3 62.8 + - - +
716B GLY* 3.0 12.4 + - - -
717B LEU* 3.2 10.7 + - - +
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Residues in contact with LEU 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 VAL 2.9 17.1 + - - +
711B LEU* 4.0 4.7 - - - +
713B GLU* 1.3 77.8 - - - +
715B LYS* 1.3 51.7 + - - +
717B LEU* 3.1 8.4 + - - +
718B GLN* 2.7 36.2 + - - +
785B VAL* 5.0 10.3 - - + +
788B SER* 5.3 6.7 - - - -
789B TYR* 4.9 18.2 - - - +
792B LEU* 6.1 1.1 - - + -
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Residues in contact with LYS 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 LEU 2.9 14.1 + - - +
712B GLN* 3.2 13.9 - - - +
713B GLU 3.1 0.2 - - - -
714B LEU* 1.3 77.3 - - - +
716B GLY* 1.3 61.9 + - - +
718B GLN* 3.1 7.3 + - - +
719B GLU* 2.9 24.9 + - - +
789B TYR* 5.7 4.3 - - - -
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Residues in contact with GLY 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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556B CYS* 5.5 7.4 - - - +
712B GLN 3.0 9.1 + - - -
713B GLU* 3.0 7.9 + - - -
715B LYS* 1.3 77.9 - - - +
717B LEU* 1.3 61.1 + - - +
719B GLU* 3.3 5.6 + - - +
720B PHE* 3.0 22.7 + - - +
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Residues in contact with LEU 717 (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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556B CYS* 5.8 3.8 - - - +
713B GLU 3.2 10.2 + - - +
714B LEU* 3.1 12.2 + - - +
716B GLY* 1.3 72.6 - - - +
718B GLN* 1.3 66.7 + - - +
720B PHE* 3.0 7.6 + - - +
721B LEU* 2.9 25.0 + - - +
785B VAL* 5.4 9.4 - - + -
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Residues in contact with GLN 718 (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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714B LEU 2.7 19.8 + - - +
715B LYS* 3.5 8.7 - - - +
717B LEU* 1.3 74.1 - - - +
719B GLU* 1.3 57.6 + - - +
721B LEU* 3.4 3.8 + - - +
722B ASP* 2.9 30.9 + - - +
785B VAL* 5.0 9.9 - - - +
786B ARG* 5.2 11.2 - - + -
789B TYR* 5.0 13.7 - - + -
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Residues in contact with GLU 719 (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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715B LYS 2.9 15.0 + - - +
716B GLY* 3.7 5.8 - - - +
718B GLN* 1.3 76.7 - - - +
720B PHE* 1.3 64.2 + - - +
722B ASP* 3.2 7.1 + - - +
723B ARG* 2.9 26.0 + - - +
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Residues in contact with PHE 720 (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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556B CYS* 5.4 10.1 - - + -
716B GLY 3.0 14.9 + - - +
717B LEU* 3.3 11.9 - - - +
719B GLU* 1.3 77.9 - - - +
721B LEU* 1.3 62.6 + - - +
723B ARG* 3.2 5.6 + - - +
724B ASN* 3.0 23.4 + - - +
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Residues in contact with LEU 721 (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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717B LEU 2.9 14.9 + - - +
718B GLN* 4.0 3.6 - - - +
720B PHE* 1.3 73.8 - - - +
722B ASP* 1.3 67.7 + - - +
724B ASN* 3.3 3.3 - - - +
725B SER* 2.9 29.0 + - - -
782B GLN* 4.7 22.2 - - + -
785B VAL* 6.0 3.4 - - + -
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Residues in contact with ASP 722 (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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718B GLN 2.9 19.1 + - - +
719B GLU* 3.6 7.6 - - - +
721B LEU* 1.3 77.7 - - - +
723B ARG* 1.3 64.5 + - - +
725B SER* 3.5 14.1 + - - -
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Residues in contact with ARG 723 (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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719B GLU 2.9 17.4 + - - +
720B PHE* 3.6 5.2 - - - +
722B ASP* 1.3 80.4 - - - +
724B ASN* 1.3 58.0 + - + +
725B SER 3.3 2.6 + - - -
726B GLN* 4.6 4.0 + - - +
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Residues in contact with ASN 724 (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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720B PHE 3.0 15.3 + - - +
721B LEU* 3.3 4.8 - - - -
723B ARG* 1.3 77.7 - - + +
725B SER* 1.3 62.7 + - - +
726B GLN* 3.3 2.2 + - - +
727B PHE* 3.7 18.1 + - + +
728B ALA* 3.9 10.4 + - - +
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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