Contacts of the helix formed by residues 680 - 692 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A ALA* 3.2 0.8 - - - +
679A PRO* 1.3 96.6 - - + +
681A GLU* 1.3 63.4 + - - +
682A ALA 3.4 2.5 - - - -
683A LEU* 3.2 8.8 + - + +
684A GLN* 3.1 39.2 + - - +
700A VAL* 4.4 4.9 - - + -
702A PRO* 3.9 22.9 - - + -
706A ASP 3.6 23.6 - - - -
707A GLN* 4.7 9.6 - - + -
710A PRO* 4.2 3.6 - - + -
714A HIS* 3.7 33.9 - + - -
716A PHE* 3.7 31.6 - + - -
729A HIS* 3.9 23.6 - + - -
731A PRO* 4.6 2.7 - - + -
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Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ILE* 4.1 23.2 - - + +
678A ALA* 3.6 32.7 + - + +
679A PRO 3.6 0.4 - - - -
680A PHE* 1.3 77.2 - - - +
682A ALA* 1.3 58.4 + - - +
684A GLN* 3.0 23.8 + - - +
685A GLN* 2.9 58.8 + - - +
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Residues in contact with ALA 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A THR* 4.1 2.9 - - + -
652A ILE 3.4 21.3 - - - +
653A ASN* 4.0 1.9 + - - -
654A THR* 3.8 30.5 - - + +
673A ASP* 3.8 21.3 + - - +
678A ALA 5.2 0.4 + - - -
680A PHE 3.4 0.8 - - - -
681A GLU* 1.3 78.4 - - - +
683A LEU* 1.3 60.0 + - - +
685A GLN* 3.5 6.2 + - - +
686A THR* 2.8 28.5 + - - -
729A HIS* 6.1 0.4 - - + -
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Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A MET* 4.0 13.0 - - + -
654A THR* 5.5 0.4 - - + -
671A SER* 4.0 9.9 - - - +
673A ASP* 5.3 1.0 + - - -
680A PHE* 3.2 11.7 + - + +
681A GLU 3.2 0.4 - - - -
682A ALA* 1.3 80.0 - - + +
684A GLN* 1.3 56.9 + - - +
686A THR* 3.2 5.5 + - - -
687A GLU* 2.9 26.9 + - - +
697A PHE* 4.2 12.3 - - + -
700A VAL* 4.0 17.6 - - + +
716A PHE* 3.5 35.9 - - + -
727A LEU* 3.9 30.1 - - + -
729A HIS* 3.4 35.9 - - + +
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Residues in contact with GLN 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A PHE* 3.1 23.5 + - - +
681A GLU* 3.0 26.8 + - - +
683A LEU* 1.3 74.9 - - - +
685A GLN* 1.3 63.4 + - - +
687A GLU* 3.3 11.4 + - - +
688A LEU* 3.1 27.8 + - + +
700A VAL* 3.9 27.3 + - + +
702A PRO* 4.1 15.8 - - - +
707A GLN* 6.0 1.8 - - - +
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Residues in contact with GLN 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ILE* 3.7 21.5 - - + +
653A ASN* 3.3 34.7 + - - +
681A GLU* 2.9 39.7 + - - +
682A ALA* 3.6 6.5 - - - +
684A GLN* 1.3 74.9 - - - +
686A THR* 1.3 57.9 + - - +
688A LEU* 3.2 18.7 + - - +
689A TYR* 2.8 30.0 + - - +
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Residues in contact with THR 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A MET* 4.9 3.3 - - + +
653A ASN* 5.3 1.1 + - - +
654A THR* 3.5 7.1 - - - +
656A SER* 2.5 40.7 + - - -
660A PHE* 4.2 5.6 - - + -
682A ALA 2.8 17.1 + - - -
683A LEU* 3.2 13.9 + - + -
685A GLN* 1.3 74.7 - - - +
687A GLU* 1.3 67.2 + - - +
689A TYR* 3.6 6.8 - - - +
690A CYS* 3.0 24.9 + - - -
697A PHE* 3.4 30.7 - - + -
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Residues in contact with GLU 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A LEU 2.9 13.3 + - - +
684A GLN* 3.5 15.4 - - - +
686A THR* 1.3 77.0 - - - +
688A LEU* 1.3 53.9 + - + +
690A CYS* 3.4 1.6 + - - +
691A ARG* 2.8 67.4 + - - +
697A PHE* 3.8 24.0 - - + +
698A PRO 4.0 1.1 - - - +
699A ARG* 3.2 27.7 - - - +
700A VAL* 3.4 31.4 + - + +
701A GLU* 5.7 1.0 - - - +
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Residues in contact with LEU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A GLN* 3.1 17.6 + - + +
685A GLN* 3.4 21.1 - - - +
687A GLU* 1.3 76.8 - - + +
689A TYR* 1.3 66.7 + - - +
691A ARG* 3.2 20.9 + - - +
692A ALA* 2.9 27.6 + - - +
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Residues in contact with TYR 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A TRP* 4.2 18.7 - + - -
491A LEU* 4.6 8.0 - - - +
656A SER* 5.0 7.4 - - - +
657A PRO* 3.4 49.0 + - + +
660A PHE* 4.6 15.4 + - + +
685A GLN 2.8 21.3 + - - +
686A THR* 3.6 7.9 - - - +
688A LEU* 1.3 75.0 - - - +
690A CYS* 1.3 73.0 + - - +
692A ALA* 3.6 1.0 + - - -
693A ARG* 2.8 81.9 + - - +
695A LEU* 5.1 0.7 - - + -
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Residues in contact with CYS 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A PHE* 3.9 34.1 - - - -
686A THR* 3.0 21.7 + - - +
687A GLU 3.8 3.4 - - - +
689A TYR* 1.3 78.9 - - - +
691A ARG* 1.3 65.8 + - - +
692A ALA 3.1 2.0 - - - -
693A ARG* 2.8 12.1 + - - +
694A GLY 3.0 11.4 + - - -
695A LEU* 3.2 34.5 + - + +
697A PHE* 3.8 30.5 - - + -
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Residues in contact with ARG 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A GLU* 2.8 56.4 + - + +
688A LEU* 3.5 20.2 - - - +
690A CYS* 1.3 73.3 - - - +
692A ALA* 1.3 61.6 + - - +
693A ARG 3.2 1.0 + - - -
694A GLY* 3.4 10.3 + - - +
695A LEU 5.3 2.2 - - - +
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Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A LEU 2.9 16.4 + - - +
689A TYR* 4.0 5.2 - - - +
690A CYS 3.1 0.4 - - - -
691A ARG* 1.3 76.2 - - - +
693A ARG* 1.3 70.5 + - - +
694A GLY 3.7 0.2 - - - -
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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