Contacts of the helix formed by residues 631 - 642 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594G TRP* 3.1 62.5 + - + +
625I GLY 4.3 3.6 + - - -
626I PHE* 3.8 32.3 - - + +
627I ILE* 3.4 24.2 - - - +
628I ALA* 3.4 24.5 - - + +
629I ASP 2.9 1.4 + - - -
630I ASN* 1.3 79.5 - - - +
632I MET* 1.3 61.5 + - - +
633I ASN 3.1 1.4 + - - -
634I HIS* 3.1 13.3 + - - +
635I ALA* 3.0 18.8 + - - +
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Residues in contact with MET 632 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G PHE* 3.3 54.3 - - + -
617I TRP* 4.0 9.0 - - + -
626I PHE* 3.7 38.4 - - + -
628I ALA 4.0 2.5 - - - +
629I ASP 2.6 23.1 + - - +
631I GLN* 1.3 70.1 - - - +
633I ASN* 1.3 56.1 + - - +
635I ALA* 3.6 8.4 - - + +
636I CYS* 3.0 32.7 + - - -
663I MET* 3.5 24.0 - - + -
668I LEU* 3.6 24.2 - - + +
669I ILE* 3.9 2.4 - - - +
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Residues in contact with ASN 633 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629I ASP 5.0 0.9 - - - +
630I ASN* 4.5 11.1 - - - +
631I GLN 3.1 0.6 + - - -
632I MET* 1.3 74.9 - - - +
634I HIS* 1.3 65.1 + - - +
635I ALA 3.2 0.7 + - - -
636I CYS* 3.3 11.9 + - - +
637I MET* 3.3 20.7 + - - +
668I LEU 4.0 9.4 - - - +
669I ILE* 3.6 7.5 - - - +
670I SER* 3.4 29.1 + - - +
673I SER* 2.6 33.9 + - - +
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Residues in contact with HIS 634 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626I PHE* 5.4 3.6 - - - -
630I ASN 4.9 1.5 + - - +
631I GLN* 3.1 13.0 + - - +
633I ASN* 1.3 77.9 - - - +
635I ALA* 1.3 56.5 + - - +
637I MET* 3.5 25.6 - - + +
638I LEU* 2.9 64.2 + - + +
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Residues in contact with ALA 635 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617I TRP* 4.1 7.1 - - + -
620I HIS* 3.2 12.1 + - - -
626I PHE* 3.5 37.5 - - + -
631I GLN 3.0 14.3 + - - +
632I MET* 3.6 24.9 - - + +
633I ASN 3.1 0.4 - - - -
634I HIS* 1.3 75.2 + - - +
636I CYS* 1.3 60.1 + - - +
638I LEU* 4.3 2.2 - - - -
639I PHE* 3.0 23.6 + - - +
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Residues in contact with CYS 636 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617I TRP* 3.9 19.5 - - - -
632I MET 3.0 20.4 + - - +
633I ASN* 3.9 3.8 - - - +
635I ALA* 1.3 72.4 - - - +
637I MET* 1.3 67.5 + - - +
639I PHE* 3.3 16.0 + - - +
640I VAL* 3.4 16.8 + - - +
656I PHE* 4.8 3.1 - - + -
659I HIS* 4.8 0.7 - - - -
660I LEU* 3.8 30.7 - - + -
663I MET* 4.2 11.4 - - - -
669I ILE* 4.0 19.1 - - + -
673I SER* 5.7 4.7 - - - +
677I ALA* 4.8 8.8 - - + +
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Residues in contact with MET 637 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633I ASN* 3.3 16.9 + - - +
634I HIS* 3.5 27.8 - - + +
636I CYS* 1.3 77.8 - - - +
638I LEU* 1.3 62.9 + - + +
640I VAL* 3.0 28.5 + - - +
641I GLU* 3.2 23.2 + - - +
673I SER* 5.9 3.6 - - - +
676I LYS* 3.3 44.6 - - + +
677I ALA* 5.2 6.7 - - + +
680I LYS* 4.7 11.4 - - + +
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Residues in contact with LEU 638 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620I HIS* 3.7 11.0 - - - +
624I HIS* 3.9 30.3 - - + +
626I PHE* 4.1 16.4 - - + -
634I HIS* 2.9 57.4 + - + +
635I ALA 3.7 3.1 - - - +
637I MET* 1.3 74.8 - - + +
639I PHE* 1.3 54.6 + - - +
641I GLU* 3.2 16.9 + - + +
642I ASN* 2.7 43.4 + - - +
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Residues in contact with PHE 639 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613I VAL* 4.4 11.9 - - + -
616I LEU* 3.6 45.3 - - + -
617I TRP* 3.6 27.6 - + + -
620I HIS* 3.3 29.3 - + + +
635I ALA 3.0 17.3 + - - +
636I CYS 3.5 6.3 - - - +
637I MET 3.2 0.4 - - - -
638I LEU* 1.3 76.3 - - - +
640I VAL* 1.3 56.5 + - - +
643I TYR* 3.0 34.7 + + + +
644I GLY 3.1 5.2 + - - -
647I ILE* 3.3 27.8 - - + -
656I PHE* 3.6 31.6 - + - -
659I HIS* 4.9 1.1 - + - -
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Residues in contact with VAL 640 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636I CYS 3.4 5.1 + - - +
637I MET* 3.0 24.8 + - - +
639I PHE* 1.3 76.6 - - + +
641I GLU* 1.3 64.6 + - + +
642I ASN 3.6 0.3 - - - +
644I GLY* 2.7 32.3 + - - +
645I GLN 4.1 0.2 + - - -
647I ILE* 5.3 0.4 - - + -
656I PHE* 3.3 39.9 - - + -
677I ALA* 4.1 12.1 - - + +
680I LYS* 4.0 40.6 - - + +
681I LEU* 4.5 10.3 - - + +
684I MET* 3.9 10.2 - - + +
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Residues in contact with GLU 641 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637I MET* 3.2 26.7 + - - +
638I LEU* 3.9 18.2 - - + +
640I VAL* 1.3 75.5 - - + +
642I ASN* 1.3 69.1 + - - +
680I LYS* 3.0 42.2 + - - +
684I MET* 4.2 14.4 - - + +
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Residues in contact with ASN 642 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620I HIS* 4.5 2.7 - - - +
623I LYS* 4.4 11.1 - - - +
624I HIS* 3.9 25.5 + - - -
638I LEU* 2.7 26.0 + - - +
640I VAL 3.6 0.3 - - - +
641I GLU* 1.3 81.8 + - - +
643I TYR* 1.3 79.7 + - + +
644I GLY 3.2 1.7 + - - -
645I GLN* 4.0 9.7 + - - +
646I LYS* 5.7 0.7 - - - +
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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
------------------------------------------------------------
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