Contacts of the helix formed by residues 631 - 642 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594J TRP* 3.2 63.4 - - + +
625L GLY 5.0 0.6 + - - -
626L PHE* 4.0 33.1 - - + +
627L ILE* 3.5 24.7 - - - +
628L ALA* 3.4 25.2 - - + +
629L ASP 2.9 0.8 + - - -
630L ASN* 1.3 77.7 - - - +
632L MET* 1.3 57.2 + - - +
633L ASN 3.0 1.6 + - - -
634L HIS* 3.2 10.0 + - - +
635L ALA* 2.9 25.1 + - - +
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Residues in contact with MET 632 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J PHE* 3.5 57.4 - - + -
617L TRP* 4.1 9.2 - - + -
621L VAL* 4.9 0.2 - - + -
626L PHE* 3.7 33.4 - - + -
628L ALA 4.1 4.0 - - - +
629L ASP 2.8 23.2 + - - +
631L GLN* 1.3 69.8 - - - +
633L ASN* 1.3 61.6 + - - +
635L ALA* 3.6 6.6 - - + +
636L CYS* 3.2 17.7 + - - -
663L MET* 3.5 22.9 - - + -
668L LEU* 3.8 24.5 - - + +
669L ILE* 3.3 17.5 - - + +
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Residues in contact with ASN 633 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629L ASP 4.6 0.6 + - - -
630L ASN* 3.9 10.6 + - - +
631L GLN 3.0 0.8 + - - -
632L MET* 1.3 72.6 - - - +
634L HIS* 1.3 60.7 + - - +
635L ALA 2.9 9.0 + - - -
636L CYS* 3.1 15.1 + - - +
637L MET* 3.3 13.2 + - - +
668L LEU 4.6 2.8 + - - +
669L ILE* 3.8 10.1 - - - +
670L SER* 3.6 31.0 + - - +
673L SER* 2.7 39.4 + - - +
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Residues in contact with HIS 634 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626L PHE* 5.9 2.4 - - - -
630L ASN 4.9 1.3 + - - +
631L GLN* 3.2 9.7 + - - +
633L ASN* 1.3 77.2 - - - +
635L ALA* 1.3 56.2 + - - +
637L MET* 3.9 28.4 - - + +
638L LEU* 3.2 58.0 + - + +
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Residues in contact with ALA 635 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617L TRP* 3.9 13.3 - - + -
620L HIS* 3.3 8.7 + - - -
626L PHE* 3.7 36.3 - - + -
631L GLN 2.9 17.6 + - - +
632L MET* 3.6 15.9 - - + +
633L ASN 2.9 0.4 + - - -
634L HIS* 1.3 76.7 - - - +
636L CYS* 1.3 59.7 + - - +
637L MET 3.3 0.2 - - - -
639L PHE* 3.1 26.3 + - - +
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Residues in contact with CYS 636 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617L TRP* 3.8 20.4 - - - -
632L MET 3.2 16.8 + - - +
633L ASN* 3.1 5.9 + - - +
635L ALA* 1.3 76.9 - - - +
637L MET* 1.3 64.2 + - - +
639L PHE* 3.4 17.9 + - - +
640L VAL* 3.5 14.2 + - - +
656L PHE* 4.6 2.3 - - - -
659L HIS* 4.6 3.1 - - - -
660L LEU* 3.5 33.4 - - + -
663L MET* 4.4 9.9 - - - -
669L ILE* 4.3 16.2 - - + -
673L SER* 5.9 3.8 - - - +
677L ALA* 4.7 8.6 - - + +
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Residues in contact with MET 637 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633L ASN 3.3 10.6 + - - +
634L HIS* 3.9 34.3 - - + +
636L CYS* 1.3 73.4 - - - +
638L LEU* 1.3 65.0 + - + +
640L VAL* 3.1 23.7 - - - +
641L GLU* 3.3 23.9 + - - +
673L SER* 6.1 0.7 - - - -
676L LYS* 3.8 35.7 - - + +
677L ALA* 5.2 7.1 - - + +
680L LYS* 3.8 25.4 - - + -
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Residues in contact with LEU 638 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620L HIS* 3.7 17.5 - - + +
624L HIS* 4.1 28.0 - - + +
626L PHE* 4.5 12.8 - - + -
634L HIS* 3.2 45.9 + - + +
636L CYS 3.5 0.2 - - - -
637L MET* 1.3 78.0 - - + +
639L PHE* 1.3 58.1 + - - +
641L GLU* 4.2 18.8 - - - +
642L ASN* 3.0 45.0 + - - +
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Residues in contact with PHE 639 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613L VAL* 4.5 9.6 - - + -
616L LEU* 3.4 31.0 - - + -
617L TRP* 3.5 45.3 - + + -
620L HIS* 3.8 21.3 - + + +
635L ALA 3.1 19.1 + - - +
636L CYS 3.5 6.1 - - - +
637L MET 3.2 0.4 - - - -
638L LEU* 1.3 76.9 - - - +
640L VAL* 1.3 56.0 + - - +
643L TYR* 3.4 20.1 + - + +
644L GLY* 3.3 14.7 + - - -
647L ILE* 3.4 28.7 - - + -
656L PHE* 3.4 33.2 - + - -
659L HIS* 4.6 2.7 - + - -
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Residues in contact with VAL 640 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636L CYS 3.5 4.7 + - - +
637L MET* 3.1 22.2 - - - +
639L PHE* 1.3 78.9 - - + +
641L GLU* 1.3 67.5 + - - +
642L ASN 3.2 0.9 - - - -
644L GLY* 2.9 27.1 + - - +
645L GLN 3.8 0.3 + - - -
647L ILE* 5.5 0.9 - - + -
656L PHE* 3.2 42.0 - - + -
677L ALA* 4.4 6.1 - - + +
680L LYS* 3.9 32.1 - - + +
681L LEU* 4.4 21.3 - - + +
684L MET* 3.8 10.9 - - + +
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Residues in contact with GLU 641 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637L MET* 3.3 31.3 + - - +
638L LEU* 3.9 19.6 + - - +
640L VAL* 1.3 79.8 - - + +
642L ASN* 1.3 70.6 + - - +
645L GLN* 5.2 2.4 + - - +
680L LYS* 3.3 34.5 + - - +
684L MET* 4.1 17.8 - - + +
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Residues in contact with ASN 642 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620L HIS* 4.4 2.3 + - + -
623L LYS* 5.6 1.0 - - - +
624L HIS* 3.8 26.3 + - - -
638L LEU* 3.0 27.1 + - - +
640L VAL 3.9 0.2 - - - +
641L GLU* 1.3 87.8 - - - +
643L TYR* 1.3 82.6 + - + +
644L GLY 3.3 0.5 + - - -
645L GLN* 4.0 12.3 + - - +
646L LYS* 4.9 2.3 + - - +
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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