Contacts of the helix formed by residues 648 - 661 (chain J) 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 648 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646J ILE 3.7 0.2 + - - -
647J SER* 1.3 71.3 - - - +
649J ASP* 1.3 65.0 + - - +
651J ALA* 4.2 2.3 - - - +
652J ASP* 3.4 31.0 + - - +
668J ASN* 3.2 24.8 + - - -
670J ASN 3.1 23.4 + - - -
671J ASN* 3.3 25.8 + - - +
672J ASP 3.4 11.3 + - - +
673J PHE 3.6 0.8 + - - -
674J VAL* 3.2 26.1 - - + +
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Residues in contact with ASP 649 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J ASP* 4.7 1.6 - - - +
647J SER* 3.0 7.2 + - - +
648J GLN* 1.3 79.2 - - - +
650J GLU* 1.3 58.4 + - - +
651J ALA 3.2 1.1 - - - -
652J ASP* 2.8 27.9 + - - +
653J ARG* 3.3 30.1 + - - +
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Residues in contact with GLU 650 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J GLU 5.0 0.4 - - - +
124J ASP* 3.4 14.3 - - - +
125J GLU* 3.0 38.0 + - - +
153J TYR* 4.4 4.6 + - - -
646J ILE* 3.9 21.1 - - + -
647J SER* 2.8 25.5 + - - +
649J ASP* 1.3 71.2 - - - +
651J ALA* 1.3 60.6 + - - +
653J ARG* 2.5 45.8 + - - +
654J ARG* 3.1 50.8 + - - +
679J ARG* 4.8 0.2 + - - -
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Residues in contact with ALA 651 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646J ILE* 3.4 23.2 - - + +
647J SER 2.9 14.0 + - - +
648J GLN 4.4 4.0 - - - +
650J GLU* 1.3 77.5 - - - +
652J ASP* 1.3 59.4 + - - +
654J ARG* 3.5 2.2 + - - -
655J GLY* 2.8 26.7 + - - -
666J LEU* 3.6 21.8 - - + +
674J VAL* 3.9 25.8 - - + -
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Residues in contact with ASP 652 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J ASN* 5.2 2.3 + - - -
648J GLN* 3.4 18.5 + - - +
649J ASP* 2.8 19.7 + - - +
651J ALA* 1.3 76.5 - - - +
653J ARG* 1.3 56.2 + - + +
655J GLY* 3.6 2.6 - - - +
656J LYS* 3.2 29.5 + - - +
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Residues in contact with ARG 653 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J ASP* 3.1 23.8 + - - +
125J GLU 3.1 16.7 + - - -
126J THR* 5.6 3.4 - - - +
149J LEU* 4.4 6.7 - - - +
152J ASN* 3.7 34.5 + - + +
153J TYR* 3.4 40.2 + - + +
649J ASP* 3.5 19.6 + - - +
650J GLU* 2.5 51.1 + - - +
651J ALA 3.2 0.4 - - - -
652J ASP* 1.3 73.8 - - + +
654J ARG* 1.3 65.2 + - - +
655J GLY 3.0 1.3 - - - -
656J LYS* 3.2 16.3 + - - +
657J VAL* 3.2 12.0 + - - +
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Residues in contact with ARG 654 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J VAL* 4.3 12.9 - - - +
123J GLU 5.2 1.0 + - - -
125J GLU* 5.9 0.4 - - - +
153J TYR* 4.3 5.1 + - - +
644J GLU* 2.6 29.7 + - - -
646J ILE* 3.8 33.1 - - - +
650J GLU* 3.1 33.1 + - - +
651J ALA* 3.8 6.7 - - - +
653J ARG* 1.3 73.4 - - - +
655J GLY* 1.3 59.9 + - - +
657J VAL* 3.2 10.0 - - - +
658J TYR* 2.9 56.6 + - + +
666J LEU* 5.0 0.7 - - + -
676J ASP* 3.0 26.0 + - - +
679J ARG* 3.5 39.7 - - - +
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Residues in contact with GLY 655 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651J ALA 2.8 18.2 + - - -
652J ASP* 3.6 4.7 - - - -
653J ARG 3.0 0.8 - - - -
654J ARG* 1.3 74.1 - - - +
656J LYS* 1.3 52.9 + - - +
658J TYR* 2.8 8.9 + - - +
659J ASP* 2.6 46.5 + - - +
664J SER* 5.9 0.9 - - - -
666J LEU* 4.4 11.7 - - - -
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Residues in contact with LYS 656 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J PHE* 3.6 23.9 - - + -
148J GLU* 3.1 45.0 + - - +
149J LEU* 4.5 9.9 - - + -
152J ASN* 3.1 30.3 - - - +
652J ASP 3.2 13.4 + - - +
653J ARG 3.2 9.0 + - - +
655J GLY* 1.3 73.3 - - - +
657J VAL* 1.3 62.9 + - - +
659J ASP* 3.5 15.0 + - - +
660J LYS* 3.4 12.6 + - - +
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Residues in contact with VAL 657 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J PRO* 3.7 29.6 - - + -
134J MET* 6.3 0.4 - - - -
145J PHE* 4.6 7.4 - - + -
149J LEU* 4.6 13.1 - - + +
653J ARG 3.2 6.9 + - - +
654J ARG* 3.2 24.7 - - + +
655J GLY 3.1 0.8 - - - -
656J LYS* 1.3 78.5 - - - +
658J TYR* 1.3 79.6 + - + +
660J LYS* 3.0 14.4 + - + +
661J TYR* 3.3 29.3 - - + -
809J 74D 4.4 15.5 - - + -
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Residues in contact with TYR 658 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654J ARG* 2.9 45.6 + - + +
655J GLY 2.8 8.0 + - - +
657J VAL* 1.3 85.9 - - + +
659J ASP* 1.3 62.1 + - - +
661J TYR* 3.1 14.9 + - - +
662J MET 3.3 4.5 + - - -
663J CYS 3.1 21.2 + - - +
664J SER* 3.5 36.1 - - - -
665J PHE 4.6 0.4 - - - -
666J LEU* 4.0 13.7 - - + -
676J ASP* 2.8 29.2 + - - -
678J THR* 3.5 37.8 - - + +
679J ARG* 5.0 3.1 + - - +
809J 74D 3.8 25.5 - - + -
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Residues in contact with ASP 659 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655J GLY* 2.6 32.8 + - - +
656J LYS* 3.5 17.9 + - - +
657J VAL 3.2 0.2 - - - -
658J TYR* 1.3 73.5 - - - +
660J LYS* 1.3 59.1 + - + +
662J MET* 3.2 25.2 + - - +
664J SER* 5.3 5.5 + - - -
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Residues in contact with LYS 660 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J MET* 3.9 22.7 - - - +
141J GLN 5.9 1.2 + - - -
142J ASP 6.1 3.3 - - - +
145J PHE* 3.6 63.5 - - + -
656J LYS 3.4 1.8 + - - +
657J VAL* 3.0 13.2 + - + +
659J ASP* 1.3 79.7 - - + +
661J TYR* 1.3 58.8 + - + +
662J MET* 3.3 14.1 + - - +
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Residues in contact with TYR 661 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J TYR* 4.6 11.2 - - - -
132J PRO* 3.6 20.3 - - - +
133J TYR 4.3 5.7 + - - -
134J MET* 3.8 28.5 - - + +
657J VAL* 3.3 30.5 - - + -
658J TYR* 3.1 9.1 + - - +
660J LYS* 1.3 75.3 - - - +
662J MET* 1.3 65.3 + - - +
663J CYS* 2.9 17.6 + - - +
809J 74D 3.5 71.5 - + + +
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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