Contacts of the helix formed by residues 668 - 677 (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 ASP 668 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B ALA* 3.4 6.4 + - - -
666B ALA* 3.1 6.0 - - + -
667B GLU* 1.3 72.5 - - - +
669B ASP* 1.3 54.5 + - - +
670B ASN* 3.5 6.7 - - - +
671B LEU* 2.7 44.9 + - + +
672B MET* 2.6 37.0 + - - +
743B PHE* 3.4 20.8 - - - -
744B PRO* 3.7 1.5 - - - +
745B GLY* 2.6 42.1 + - - -
746B VAL* 3.1 15.9 + - + +
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Residues in contact with ASP 669 (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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667B GLU 3.1 11.9 + - - +
668B ASP* 1.3 70.7 - - - +
670B ASN* 1.3 62.8 + - - +
672B MET* 3.1 28.6 + - - +
673B GLU* 3.3 24.8 + - - +
676B ARG* 5.2 2.2 + - - +
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Residues in contact with ASN 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ASP* 3.2 9.7 + - - +
669B ASP* 1.3 77.4 - - - +
671B LEU* 1.3 62.6 + - - +
673B GLU* 3.2 21.3 + - - +
674B ALA* 3.3 6.6 + - - +
684B LYS* 5.7 2.6 + - - -
742B SER* 3.2 29.4 + - - +
743B PHE* 3.1 18.8 - - - -
744B PRO* 5.2 3.6 - - + -
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Residues in contact with LEU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B LEU* 3.9 23.8 - - + +
662B LEU* 4.6 5.6 - - + -
663B ALA* 3.8 13.9 - - + +
668B ASP* 2.7 26.9 + - + +
670B ASN* 1.3 68.4 - - - +
672B MET* 1.3 63.5 + - - +
673B GLU 2.9 5.6 + - - -
674B ALA* 3.2 11.6 + - + +
675B PHE* 3.2 44.4 - - + -
681B ILE* 3.9 16.6 - - + -
743B PHE* 3.6 30.5 - - + -
746B VAL* 4.0 24.7 - - + -
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Residues in contact with MET 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B ALA* 3.5 29.6 - - + +
667B GLU* 4.0 18.4 - - + +
668B ASP 2.6 28.5 + - - +
669B ASP* 3.1 33.7 - - - +
670B ASN 3.3 0.4 - - - -
671B LEU* 1.3 73.2 - - - +
673B GLU* 1.3 57.4 + - - +
675B PHE 4.0 0.2 - - - -
676B ARG* 3.1 58.1 + - - +
859B ARG* 3.9 31.2 - - - -
860B VAL* 3.6 16.2 - - + +
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Residues in contact with GLU 673 (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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669B ASP 3.3 13.3 + - - +
670B ASN* 3.2 12.9 + - - +
671B LEU 2.9 0.4 - - - -
672B MET* 1.3 75.3 - - - +
674B ALA* 1.3 68.1 + - - +
675B PHE 2.9 1.8 - - - -
676B ARG* 2.8 25.6 + - - +
677B ARG* 2.8 76.3 + - - +
679B LEU* 5.1 0.2 - - - -
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Residues in contact with ALA 674 (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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670B ASN* 3.3 7.4 + - - +
671B LEU* 3.2 15.9 + - + +
673B GLU* 1.3 78.1 - - - +
675B PHE* 1.3 58.3 + - + +
679B LEU* 2.7 54.3 + - + +
681B ILE* 3.2 38.8 - - + -
684B LYS* 5.8 1.3 - - - +
743B PHE* 5.2 1.8 - - + -
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Residues in contact with PHE 675 (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* 3.2 39.9 - - + -
659B LEU* 3.1 45.5 - - + -
660B ARG* 3.4 40.3 + - + +
663B ALA* 4.1 9.4 - - + -
671B LEU* 3.2 43.8 + - + -
673B GLU 2.9 1.2 - - - -
674B ALA* 1.3 77.1 - - - +
676B ARG* 1.3 63.2 + - - +
677B ARG 3.3 0.9 - - - -
678B ASP* 3.2 14.9 + - - +
679B LEU 4.4 3.8 - - - -
681B ILE* 4.0 6.7 - - + -
860B VAL* 4.1 17.3 - - + -
861B PRO* 3.4 17.3 - - - +
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Residues in contact with ARG 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B ASP* 5.2 2.4 + - - -
672B MET* 3.1 54.2 + - - +
673B GLU* 2.8 28.9 + - - +
675B PHE* 1.3 73.4 - - - +
677B ARG* 1.3 59.6 + - + +
678B ASP* 2.8 13.3 + - - +
859B ARG* 3.3 27.2 + - - +
860B VAL* 4.6 0.4 - - + -
861B PRO* 4.4 19.4 - - + +
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Residues in contact with ARG 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B GLU* 2.8 46.4 + - - +
676B ARG* 1.3 74.9 - - + +
678B ASP* 1.3 65.7 + - - +
679B LEU* 2.9 46.1 + - + +
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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