Contacts of the helix formed by residues 680 - 692 (chain B) in PDB entry 5IXC
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 PHE 680 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678B ALA* 3.2 0.8 - - - +
679B PRO* 1.3 96.2 - - + +
681B GLU* 1.3 64.8 + - - +
682B ALA 3.4 2.7 - - - -
683B LEU* 3.2 9.0 + - + +
684B GLN* 3.1 38.6 + - - +
700B VAL* 4.4 4.9 - - + -
702B PRO* 3.9 22.4 - - + -
706B ASP 3.6 23.1 - - - -
707B GLN* 4.7 9.6 - - + -
710B PRO* 4.2 3.8 - - + -
714B HIS* 3.7 34.3 - + - -
716B PHE* 3.7 32.1 - + - -
729B HIS* 3.9 22.7 - + - -
731B PRO* 4.7 3.1 - - + -
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Residues in contact with GLU 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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652B ILE* 4.0 25.0 - - + +
678B ALA* 3.6 32.5 + - + +
679B PRO 3.6 0.4 - - - -
680B PHE* 1.3 76.5 - - - +
682B ALA* 1.3 59.3 + - - +
684B GLN* 3.0 23.9 + - - +
685B GLN* 2.9 57.7 + - - +
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Residues in contact with ALA 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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328B THR* 4.1 2.7 - - + -
652B ILE 3.4 21.5 + - - +
653B ASN* 4.0 1.5 + - - -
654B THR* 3.8 31.2 + - + +
673B ASP* 3.8 21.3 + - - +
678B ALA 5.2 0.2 + - - -
680B PHE 3.4 0.8 - - - -
681B GLU* 1.3 79.2 - - - +
683B LEU* 1.3 60.2 + - - +
685B GLN* 3.5 7.1 + - - +
686B THR* 2.8 28.5 + - - -
729B HIS* 6.1 0.4 - - + -
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Residues in contact with LEU 683 (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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326B MET* 4.0 12.3 - - + -
654B THR* 5.5 0.9 - - + -
671B SER* 4.0 9.6 - - - +
673B ASP* 5.3 1.2 + - - -
680B PHE* 3.2 12.3 + - + +
681B GLU 3.1 0.4 - - - -
682B ALA* 1.3 79.3 - - - +
684B GLN* 1.3 57.1 + - - +
686B THR* 3.2 5.5 + - - -
687B GLU* 2.9 26.9 + - - +
697B PHE* 4.2 12.0 - - + -
700B VAL* 4.0 18.1 - - + +
716B PHE* 3.5 35.7 - - + -
727B LEU* 3.9 30.3 - - + -
729B HIS* 3.4 36.5 - - + +
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Residues in contact with GLN 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B PHE* 3.1 24.3 + - - +
681B GLU* 3.0 27.6 + - - +
683B LEU* 1.3 75.6 - - - +
685B GLN* 1.3 63.2 + - - +
687B GLU* 3.3 11.6 + - - +
688B LEU* 3.1 28.0 + - + +
700B VAL* 3.9 28.1 + - + +
702B PRO* 4.1 15.8 - - - +
707B GLN* 6.0 1.4 - - - +
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Residues in contact with GLN 685 (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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652B ILE* 4.5 12.7 - - + +
653B ASN* 3.4 33.0 + - - +
681B GLU* 2.9 39.1 + - - +
682B ALA* 3.6 8.1 - - - +
684B GLN* 1.3 75.6 - - - +
686B THR* 1.3 57.7 + - - +
688B LEU* 3.2 19.0 + - - +
689B TYR* 2.9 29.8 + - - +
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Residues in contact with THR 686 (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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326B MET* 4.9 3.3 - - + +
653B ASN* 5.7 0.9 + - - -
654B THR* 3.5 6.8 - - - +
656B SER* 2.5 40.9 + - - -
660B PHE* 4.2 6.1 - - + -
682B ALA 2.8 17.4 + - - -
683B LEU* 3.2 14.1 + - + -
685B GLN* 1.3 74.6 - - - +
687B GLU* 1.3 66.4 + - - +
689B TYR* 3.6 6.8 - - - +
690B CYS* 3.0 25.0 + - - -
697B PHE* 3.4 30.7 - - + -
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Residues in contact with GLU 687 (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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683B LEU 2.9 12.9 + - - +
684B GLN* 3.5 14.9 - - - +
685B GLN 3.3 0.2 - - - -
686B THR* 1.3 77.1 - - - +
688B LEU* 1.3 54.7 + - + +
690B CYS* 3.3 1.6 + - - +
691B ARG* 2.8 66.2 + - + +
697B PHE* 3.8 20.9 - - + +
698B PRO 4.0 4.2 - - - +
699B ARG* 3.2 27.8 - - - +
700B VAL* 3.4 31.2 + - + +
701B GLU* 5.6 0.7 - - - +
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Residues in contact with LEU 688 (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 GLN 3.1 15.3 + - - +
685B GLN* 3.4 20.9 - - - +
687B GLU* 1.3 82.4 - - + +
689B TYR* 1.3 63.9 + - - +
691B ARG* 3.2 20.9 + - - +
692B ALA* 2.9 27.1 + - - +
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Residues in contact with TYR 689 (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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480B TRP* 4.2 18.5 - + - -
491B LEU* 4.6 7.8 - - - +
656B SER* 5.1 7.9 - - - +
657B PRO* 3.4 49.1 + - + +
660B PHE* 4.6 16.0 + - + +
685B GLN 2.9 17.9 + - - +
686B THR* 3.6 7.6 - - - +
688B LEU* 1.3 77.4 - - - +
690B CYS* 1.3 73.0 + - - +
692B ALA* 3.6 4.7 + - - -
693B ARG* 2.8 77.7 + - - +
695B LEU* 5.1 0.7 - - + -
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Residues in contact with CYS 690 (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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660B PHE* 3.9 33.7 - - - -
686B THR* 3.0 20.7 + - - +
687B GLU 3.8 2.9 - - - +
689B TYR* 1.3 79.5 - - - +
691B ARG* 1.3 65.6 + - - +
692B ALA 3.1 2.0 - - - -
693B ARG 2.9 12.0 + - - -
694B GLY 3.0 10.6 + - - -
695B LEU* 3.2 35.5 + - + +
697B PHE* 3.8 31.2 - - + -
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Residues in contact with ARG 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B GLU* 2.8 57.4 + - + +
688B LEU* 3.5 20.5 - - - +
690B CYS* 1.3 72.7 - - - +
692B ALA* 1.3 62.3 + - - +
693B ARG 3.2 1.0 + - - -
694B GLY* 3.4 9.9 + - - -
695B LEU 5.2 2.0 - - - +
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Residues in contact with ALA 692 (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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688B LEU 2.9 16.2 + - - +
689B TYR* 3.9 5.6 - - - +
690B CYS 3.1 0.4 - - - -
691B ARG* 1.3 75.9 - - - +
693B ARG* 1.3 69.7 + - - +
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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