Contacts of the helix formed by residues 683 - 687 (chain D) 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 LYS 683 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TRP* 4.5 5.9 - - + -
613D HIS* 5.6 0.6 - - - +
614D LEU* 2.7 44.4 + - + +
616D LEU* 5.4 6.7 - - + -
626D ILE* 3.0 30.0 - - + +
682D ASN* 1.3 73.9 - - - +
684D ILE* 1.3 62.7 + - - +
685D ARG 3.1 1.0 + - - -
686D PHE* 3.3 18.8 + - + -
568F SER* 3.7 36.3 - - - +
581F VAL* 5.4 9.9 - - - +
582F ASP* 6.1 1.0 - - - +
586F GLU* 4.2 24.8 + - - -
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Residues in contact with ILE 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614D LEU* 3.5 25.9 - - + +
626D ILE* 4.3 5.6 - - + +
638D ILE* 4.1 11.2 - - + -
639D SER* 4.2 9.0 - - - -
640D GLU 3.8 2.0 - - - +
641D TYR* 3.7 33.0 - - + +
682D ASN* 3.1 30.4 + - - +
683D LYS* 1.3 71.7 - - - +
685D ARG* 1.3 55.4 + - - +
686D PHE 2.7 18.1 + - - -
687D ALA* 2.8 25.7 + - + +
710D ILE* 4.2 25.1 - - + -
722D LEU* 4.1 22.4 - - + -
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Residues in contact with ARG 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D MET* 4.6 0.8 - - - +
111D TYR 4.0 7.5 + - - -
113D TRP* 3.1 60.4 - - - +
641D TYR* 3.9 22.4 + - + +
665D PHE* 4.3 7.9 - - + -
677D ALA* 2.5 56.5 + - + +
678D THR* 2.8 17.8 + - - +
681D GLY* 4.5 0.2 - - - -
682D ASN* 3.0 25.2 + - - +
684D ILE* 1.3 77.9 - - - +
686D PHE* 1.3 72.7 + - + +
687D ALA 3.3 10.9 + - - +
726D TYR* 4.7 0.5 + - - -
809D 74D 3.2 52.4 + - - +
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Residues in contact with PHE 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D MET* 4.0 26.5 - - + -
113D TRP* 3.5 37.9 - + - -
616D LEU* 4.2 17.0 - - + -
624D TRP* 3.8 13.0 - - + +
625D GLY* 3.4 16.0 - - - +
626D ILE* 3.2 35.0 + - + -
683D LYS* 3.3 24.9 - - + +
684D ILE 2.7 4.6 + - - -
685D ARG* 1.3 92.6 - - + +
687D ALA* 1.3 60.1 + - - -
688D ASN* 3.4 2.4 + - - -
809D 74D 3.2 42.8 - + - +
568F SER* 5.3 1.6 - - - -
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Residues in contact with ALA 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626D ILE* 3.4 8.9 - - + +
684D ILE* 2.8 26.5 + - + +
685D ARG 3.3 5.6 - - - +
686D PHE* 1.3 71.2 - - - +
688D ASN* 1.3 53.8 + - - +
710D ILE* 5.9 1.3 - - + -
722D LEU* 3.5 24.2 - - + +
724D PHE* 3.6 29.9 - - + -
726D TYR* 2.7 27.2 + - - -
809D 74D 4.1 1.0 - - - +
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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