Contacts of the helix formed by residues 671 - 683 (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 ILE 671 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308G ARG* 4.4 2.9 - - - +
312G GLU* 5.3 14.8 - - + +
446G THR* 3.8 23.6 - - - +
447G TYR* 3.4 48.5 + - + +
664I HIS* 3.7 24.3 + - + +
670I SER* 1.3 72.4 - - - +
672I MET* 1.3 72.9 + - + +
674I ILE* 3.1 26.9 + - + +
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Residues in contact with MET 672 (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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670I SER* 3.2 26.7 - - - +
671I ILE* 1.3 83.6 - - + +
673I SER* 1.3 58.9 + - - +
675I ASP* 3.2 9.5 + - - +
676I LYS* 3.0 28.9 + - + +
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Residues in contact with SER 673 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633I ASN* 2.6 37.7 + - - +
636I CYS* 5.7 4.0 - - - +
637I MET* 5.9 3.9 - - - +
660I LEU* 5.1 1.0 - - - +
669I ILE* 4.2 13.0 - - - -
670I SER* 2.9 18.3 + - - -
672I MET* 1.3 76.6 - - - +
674I ILE* 1.3 64.6 + - - +
676I LYS* 4.1 8.8 - - - +
677I ALA* 3.1 26.5 + - - +
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Residues in contact with ILE 674 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G LEU* 5.4 0.4 - - + -
446G THR* 5.5 2.5 - - + +
447G TYR* 3.7 12.1 - - + +
457G LEU* 3.4 26.2 - - + -
657I MET* 5.2 5.4 - - + -
660I LEU* 4.3 24.2 - - + +
661I VAL* 4.9 11.0 - - + +
664I HIS* 3.7 26.9 - - + -
669I ILE* 4.0 15.9 - - + -
671I ILE* 3.1 40.4 + - + +
673I SER* 1.3 77.5 - - - +
675I ASP* 1.3 58.3 + - - +
677I ALA* 3.7 1.0 - - - +
678I VAL* 2.8 44.9 + - + +
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Residues in contact with ASP 675 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G TYR* 4.0 7.6 + - + +
456G ARG* 3.0 36.9 + - - +
457G LEU* 3.2 29.3 - - + +
671I ILE 4.0 1.4 + - - -
672I MET* 3.2 9.9 + - - +
674I ILE* 1.3 78.1 - - - +
676I LYS* 1.3 57.4 + - - +
677I ALA 3.0 1.2 + - - -
678I VAL* 3.1 1.6 + - - +
679I THR* 2.7 45.8 + - - -
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Residues in contact with LYS 676 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637I MET* 3.3 42.5 - - + +
672I MET* 3.0 18.1 + - + +
673I SER* 4.6 7.6 - - - +
675I ASP* 1.3 75.8 + - - +
677I ALA* 1.3 56.3 + - - +
679I THR* 4.5 5.7 - - - -
680I LYS* 3.4 37.5 + - + +
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Residues in contact with ALA 677 (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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636I CYS* 4.8 16.6 - - + +
637I MET* 5.2 5.6 - - + +
640I VAL* 4.1 8.6 - - + +
656I PHE* 4.6 9.2 - - + -
660I LEU* 4.3 17.7 - - + -
673I SER* 3.1 20.4 + - - +
674I ILE 3.8 1.6 - - - +
675I ASP 3.0 1.0 - - - -
676I LYS* 1.3 76.8 - - - +
678I VAL* 1.3 55.5 + - - +
679I THR 3.3 1.6 - - - -
680I LYS* 3.2 7.2 + - - +
681I LEU* 2.7 32.9 + - - +
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Residues in contact with VAL 678 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G LEU* 4.6 11.9 - - + +
656I PHE* 5.0 3.8 - - + -
657I MET* 3.9 35.4 - - + -
660I LEU* 3.8 19.5 - - + -
674I ILE* 2.8 32.8 + - + +
675I ASP* 4.0 3.8 - - - +
677I ALA* 1.3 68.4 - - - +
679I THR* 1.3 61.8 + - - +
681I LEU* 3.4 9.2 + - + +
682I ARG* 3.0 58.6 + - + +
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Residues in contact with THR 679 (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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456G ARG* 2.9 34.2 + - - +
675I ASP* 2.7 29.5 + - - -
676I LYS* 4.5 5.2 - - - +
678I VAL* 1.3 77.1 - - - +
680I LYS* 1.3 51.7 + - + +
682I ARG* 2.9 9.4 + - - +
683I GLU* 2.6 49.9 + - + +
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Residues in contact with LYS 680 (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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637I MET* 4.7 16.0 - - + +
640I VAL* 4.0 15.5 - - + +
641I GLU* 3.0 45.5 + - - +
676I LYS* 3.4 30.9 + - + +
677I ALA* 3.2 7.4 + - - +
679I THR* 1.3 78.2 - - + +
681I LEU* 1.3 58.8 + - - +
683I GLU* 4.1 19.3 - - - +
684I MET* 3.5 30.3 + - - +
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Residues in contact with LEU 681 (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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640I VAL* 4.5 5.8 - - + +
644I GLY* 3.9 28.9 - - - +
647I ILE* 4.3 12.8 - - + -
648I ILE* 3.8 18.9 - - + +
653I CYS* 3.8 34.5 - - + +
656I PHE* 4.0 26.9 - - + -
657I MET* 5.4 1.3 - - + -
677I ALA 2.7 16.9 + - - +
678I VAL* 3.4 15.9 - - + +
680I LYS* 1.3 74.5 - - - +
682I ARG* 1.3 73.3 + - + +
684I MET* 3.0 28.9 + - + +
685I GLN* 5.0 0.4 - - - +
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Residues in contact with ARG 682 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456G ARG* 2.7 34.6 + - - +
457G LEU* 3.7 16.2 + - - +
458G ILE 3.7 12.5 + - - -
459G GLY* 3.7 9.9 - - - -
653I CYS* 6.5 0.4 - - - -
657I MET* 4.3 7.4 - - - +
678I VAL* 3.0 34.2 + - + +
679I THR* 2.9 7.9 + - - +
681I LEU* 1.3 81.6 - - + +
683I GLU* 1.3 56.5 + - - +
684I MET 3.1 5.4 - - - -
685I GLN* 3.0 47.5 + - + +
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Residues in contact with GLU 683 (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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563D LYS* 5.5 8.0 - - - +
587D THR* 5.0 10.7 - - - +
679I THR* 2.6 33.5 + - + +
680I LYS* 4.2 19.5 - - + +
682I ARG* 1.3 70.8 - - - +
684I MET* 1.3 57.2 + - - +
685I GLN 3.5 2.6 + - - -
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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