Contacts of the helix formed by residues 631 - 643 (chain C) in PDB entry 5LS6
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 GLN 631 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A TRP* 3.1 77.9 - - + +
597A LYS* 6.1 0.2 - - - +
625C GLY 4.8 1.2 + - - -
626C PHE* 3.5 34.0 - - + +
627C ILE* 3.4 24.2 - - - +
628C ALA* 3.3 17.2 - - + +
629C ASP 3.1 0.8 - - - -
630C ASN* 1.3 77.7 - - - +
632C MET* 1.3 52.9 + - - +
633C ASN 2.8 0.5 + - - -
634C HIS* 2.7 37.9 + - + +
635C ALA* 3.1 8.2 + - - -
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Residues in contact with MET 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE* 3.4 47.1 - - + -
617C TRP* 3.9 11.9 - - + -
621C VAL* 4.6 0.4 - - + -
626C PHE* 3.6 31.9 - - + -
628C ALA 4.3 2.0 - - - +
629C ASP 3.1 16.6 + - - +
631C GLN* 1.3 76.7 - - - +
633C ASN* 1.3 57.4 + - - +
635C ALA* 3.5 6.2 - - + +
636C CYS* 2.8 32.6 + - - +
663C MET* 3.5 23.8 - - + -
668C LEU* 3.9 33.9 - - + +
669C ILE* 4.2 5.4 - - + -
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Residues in contact with ASN 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629C ASP 4.7 1.7 - - - +
630C ASN* 4.6 10.7 - - - +
631C GLN 2.8 4.9 + - - -
632C MET* 1.3 71.8 - - - +
634C HIS* 1.3 62.8 + - - +
636C CYS* 3.1 5.5 + - - +
637C MET* 3.0 28.8 + - - +
668C LEU 3.4 14.0 - - - +
669C ILE* 3.6 11.7 - - - +
670C SER* 3.3 28.2 + - - +
673C SER* 2.7 32.0 + - - +
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Residues in contact with HIS 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626C PHE* 5.1 6.2 - - + -
630C ASN 4.9 1.9 + - - +
631C GLN* 2.7 17.7 + - + +
633C ASN* 1.3 75.7 - - - +
635C ALA* 1.3 57.1 + - - +
637C MET* 3.3 32.0 - - + +
638C LEU* 2.9 59.6 + - + +
641C GLU* 5.8 0.6 + - - -
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Residues in contact with ALA 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C TRP* 3.9 10.1 - - + -
620C HIS* 3.3 6.7 + - - -
626C PHE* 3.2 46.1 - - + -
631C GLN 3.1 6.3 + - - +
632C MET* 3.5 24.2 - - + +
634C HIS* 1.3 74.6 + - - +
636C CYS* 1.3 59.6 + - - +
638C LEU* 4.4 0.7 - - - +
639C PHE* 3.0 27.7 + - - +
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Residues in contact with CYS 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C TRP* 4.2 16.8 - - - -
632C MET 2.8 15.4 + - - +
633C ASN* 3.1 6.5 + - - +
635C ALA* 1.3 70.2 - - - +
637C MET* 1.3 66.9 + - - +
639C PHE* 3.5 14.1 + - - +
640C VAL* 3.6 16.5 + - - +
656C PHE* 5.1 1.9 - - - -
659C HIS* 4.7 3.6 - - - -
660C LEU* 3.7 30.1 - - + -
663C MET* 4.5 8.1 - - - -
669C ILE* 3.9 27.6 - - + -
673C SER* 5.3 5.8 - - - -
677C ALA* 4.7 10.1 - - + +
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Residues in contact with MET 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C ASN* 3.0 20.1 + - - +
634C HIS* 3.3 36.3 - - + +
636C CYS* 1.3 75.4 - - + +
638C LEU* 1.3 63.3 + - - +
640C VAL* 3.2 26.3 + - - +
641C GLU* 3.2 24.8 + - - +
673C SER* 6.0 3.8 - - - +
676C LYS* 4.0 30.3 - - + +
677C ALA* 5.5 4.7 - - + +
680C LYS* 5.3 9.2 - - + +
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Residues in contact with LEU 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C HIS* 3.7 15.0 - - + +
624C HIS* 3.7 31.0 - - + +
626C PHE* 4.5 8.7 - - + -
634C HIS* 2.9 45.4 + - + +
635C ALA* 4.5 0.4 - - - -
637C MET* 1.3 69.9 - - - +
639C PHE* 1.3 66.6 + - - +
641C GLU* 3.5 25.9 + - + +
642C ASN* 3.1 38.7 + - - +
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Residues in contact with PHE 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C VAL* 4.4 8.1 - - + -
616C LEU* 3.6 18.8 - - + -
617C TRP* 3.6 61.9 - + + -
620C HIS* 3.6 21.7 - + + +
635C ALA 3.0 19.0 + - - +
636C CYS 3.6 6.3 - - - +
637C MET 3.2 0.4 - - - -
638C LEU* 1.3 76.3 - - - +
640C VAL* 1.3 56.3 + - + +
643C TYR* 2.9 38.5 + - + +
644C GLY 3.3 4.7 + - - -
647C ILE* 3.4 30.3 - - + -
656C PHE* 3.6 30.1 - + - -
659C HIS* 5.3 1.6 - + - -
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Residues in contact with VAL 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636C CYS 3.6 7.8 + - - +
637C MET* 3.2 16.5 + - - +
639C PHE* 1.3 76.6 - - + +
641C GLU* 1.3 60.6 + - - +
642C ASN 3.1 6.8 + - - +
644C GLY* 3.3 24.3 + - - +
645C GLN 4.4 0.3 + - - -
647C ILE* 5.6 0.4 - - + -
656C PHE* 3.3 39.7 - - + -
677C ALA* 4.1 14.6 - - + +
680C LYS* 4.0 33.7 - - + +
681C LEU* 4.6 15.9 - - + +
684C MET* 4.0 14.6 - - + +
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Residues in contact with GLU 641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634C HIS* 5.8 0.5 + - - -
637C MET* 3.2 42.2 + - - +
638C LEU* 3.3 27.0 + - + +
640C VAL* 1.3 75.6 - - - +
642C ASN* 1.3 70.6 + - - +
680C LYS* 3.8 27.1 - - - +
684C MET* 5.1 6.3 - - + -
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Residues in contact with ASN 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C HIS* 4.2 0.5 + - - -
624C HIS* 3.9 26.0 + - - -
638C LEU* 3.1 24.6 + - - +
641C GLU* 1.3 98.0 + - - +
643C TYR* 1.3 80.9 + - + +
644C GLY 3.4 2.3 + - - -
645C GLN* 3.8 15.2 + - - +
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Residues in contact with TYR 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C LEU* 3.5 51.0 - - + +
619C LEU* 3.9 28.2 + - + +
620C HIS* 4.0 26.3 - + - -
623C LYS* 4.2 19.1 - - + +
624C HIS* 5.3 0.2 - + - -
639C PHE* 2.9 31.2 + + + +
642C ASN* 1.3 87.3 - - + +
644C GLY* 1.3 55.4 + - - +
645C GLN 3.1 6.1 - - - -
646C LYS* 3.1 23.3 + - - +
647C ILE* 3.1 27.6 + - + +
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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