Contacts of the helix formed by residues 656 - 667 (chain B) in PDB entry 1LV5
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 656 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B DCP 3.0 33.2 + - - +
655B SER* 1.3 85.2 + - - +
657B ILE* 1.3 64.1 + - - +
658B GLU 3.4 2.5 - - - -
659B LEU* 3.0 17.2 + - + +
660B ARG* 3.0 19.7 + - - +
675B PHE* 3.2 25.7 - - + -
679B LEU 3.2 19.8 + - - -
680B ASP* 3.3 17.9 + - - +
681B ILE* 2.7 33.3 + - - +
682B HIS* 4.0 16.4 + - + +
702B ARG* 4.5 2.7 - - - +
863B LYS* 4.6 5.3 - - - +
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Residues in contact with ILE 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B DCP 3.0 49.2 + - - +
654B TYR* 3.8 36.8 - - + -
655B SER 2.9 5.4 + - - -
656B GLN* 1.3 76.4 - - - +
658B GLU* 1.3 61.3 + - + +
660B ARG* 3.5 3.0 + - - +
661B VAL* 3.2 31.4 + - + +
800B ALA* 4.0 19.7 - - + +
803B ILE* 4.6 10.5 - - + -
830B ASP* 4.0 11.2 - - + +
862B LEU* 4.2 20.9 - - + -
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Residues in contact with GLU 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B DCP 3.0 52.5 + - + +
615B ARG* 4.1 3.6 + - - -
657B ILE* 1.3 76.7 - - + +
659B LEU* 1.3 60.7 + - - +
661B VAL* 4.2 6.1 - - - -
662B LEU* 3.0 28.2 + - - +
710B PHE* 3.8 6.1 - - + -
714B TYR* 2.5 37.8 + - - +
793B ASN* 4.6 0.7 + - - -
796B ILE* 3.3 9.3 - - + +
797B GLN* 3.3 39.8 - - - +
800B ALA* 4.2 14.9 - - + +
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Residues in contact with LEU 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B GLN* 3.0 8.3 + - + +
658B GLU* 1.3 78.6 - - - +
660B ARG* 1.3 59.9 + - - +
662B LEU* 3.3 9.6 + - + +
663B ALA* 2.9 29.3 + - - +
671B LEU* 3.9 8.3 - - + +
675B PHE* 3.1 22.8 - - + -
681B ILE* 3.4 37.7 - - + -
682B HIS* 3.2 33.9 - - + +
709B ASN* 4.6 9.0 - - + +
710B PHE* 3.5 24.9 - - + -
713B VAL* 4.8 14.6 - - + -
739B TYR* 5.3 0.9 - - - +
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Residues in contact with ARG 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B TYR* 6.5 0.2 - - - -
655B SER* 2.9 34.1 + - - -
656B GLN* 3.0 21.8 + - - +
657B ILE* 3.8 7.2 - - - +
659B LEU* 1.3 74.5 - - - +
661B VAL* 1.3 66.6 + - - +
663B ALA* 3.2 0.9 + - - +
664B HIS* 3.0 20.8 + - - +
675B PHE* 3.4 46.7 + - + +
678B ASP* 4.2 6.5 + - - +
679B LEU 5.0 1.2 + - - -
858B LEU* 4.6 1.1 - - - -
860B VAL* 3.5 22.7 - - + +
861B PRO* 2.7 38.0 + - - +
862B LEU* 3.6 23.6 - - + +
863B LYS* 3.3 38.0 - - - +
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Residues in contact with VAL 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B ILE* 3.2 23.6 + - + +
658B GLU* 4.1 6.7 - - - +
660B ARG* 1.3 77.1 - - - +
662B LEU* 1.3 52.1 + - - +
664B HIS* 3.0 4.5 + - + +
665B ILE* 2.6 59.3 + - + +
766B LEU* 5.0 2.2 - - + -
796B ILE* 3.7 19.1 - - + +
799B SER* 3.8 9.2 - - - -
800B ALA* 4.4 8.7 - - + -
803B ILE* 3.6 30.7 - - + -
858B LEU* 4.2 12.8 - - + -
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Residues in contact with LEU 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B GLU 3.0 22.6 + - - +
659B LEU* 3.6 9.2 - - + +
660B ARG 3.2 0.2 - - - -
661B VAL* 1.3 76.9 - - - +
663B ALA* 1.3 54.7 + - - +
665B ILE* 4.3 2.5 - - - +
666B ALA* 2.6 44.0 + - + +
671B LEU* 4.6 5.8 - - + -
713B VAL* 4.0 24.0 - - + -
746B VAL* 3.5 40.2 - - + -
749B TYR* 3.9 13.0 - - + -
750B MET* 3.8 15.7 - - + -
796B ILE* 3.7 29.1 - - + +
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Residues in contact with ALA 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659B LEU 2.9 17.6 + - - +
660B ARG 3.2 4.7 + - - +
662B LEU* 1.3 75.6 - - - +
664B HIS* 1.3 57.9 + - - +
667B GLU* 2.8 28.9 + - - -
668B ASP* 3.4 7.4 + - - +
671B LEU* 3.8 25.5 - - + +
672B MET* 3.5 27.3 - - + +
675B PHE* 4.1 10.3 - - + -
860B VAL* 4.5 5.2 - - + -
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Residues in contact with HIS 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B ARG 3.0 12.8 + - - +
661B VAL* 3.3 7.9 - - - +
663B ALA* 1.3 78.9 - - - +
665B ILE* 1.3 75.5 + - + +
667B GLU* 3.2 8.3 + - - +
766B LEU* 4.2 17.5 - - + +
857B THR 4.6 3.6 - - - -
858B LEU* 3.4 38.5 - - + +
859B ARG* 2.4 91.1 + - + +
860B VAL* 4.7 1.5 - - + +
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Residues in contact with ILE 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B VAL* 2.6 42.9 + - + +
662B LEU 3.9 2.2 - - - +
664B HIS* 1.3 80.0 - - + +
666B ALA* 1.3 59.9 + - - +
667B GLU* 4.5 3.6 - - - +
749B TYR* 3.5 38.5 - - + +
766B LEU* 3.8 18.4 - - + -
795B PRO* 3.6 26.0 - - + +
796B ILE* 3.6 12.3 - - + -
799B SER* 3.7 8.5 - - - +
859B ARG* 4.4 1.8 + - - +
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Residues in contact with ALA 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B LEU* 2.6 30.5 + - + +
665B ILE* 1.3 72.7 - - - +
667B GLU* 1.3 69.8 - - - +
668B ASP* 3.1 8.5 + - + +
745B GLY* 3.9 17.7 - - - +
746B VAL* 4.3 2.9 - - - +
748B ARG* 5.6 1.4 + - - -
749B TYR* 3.5 35.8 - - + +
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Residues in contact with GLU 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B ALA 2.8 14.5 + - - -
664B HIS 3.2 13.9 + - - +
665B ILE 4.5 3.1 - - - +
666B ALA* 1.3 81.4 - - - +
668B ASP* 1.3 60.2 + - - +
669B ASP* 3.1 15.5 + - - +
672B MET* 4.0 12.6 - - + +
745B GLY* 5.6 0.3 - - - -
859B ARG* 2.8 38.8 + - - +
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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