Contacts of the helix formed by residues 717 - 725 (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 SER 717 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715B GLY 3.8 1.4 + - - -
716B ILE* 1.3 76.3 - - - +
718B ASP* 1.3 64.6 + - - +
719B TYR* 3.9 7.9 + - - +
720B GLY 3.0 9.5 + - - -
721B LEU* 2.9 26.0 + - - +
736B ILE* 3.9 2.9 - - - -
2F C 3.7 25.9 - - - -
3F G 2.5 26.8 + - - -
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Residues in contact with ASP 718 (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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717B SER* 1.3 74.8 - - - +
719B TYR* 1.3 81.1 + - - +
721B LEU 3.1 0.3 + - - -
722B ALA* 2.7 33.8 + - - +
729B ARG* 3.9 20.0 + - + +
732B ALA* 2.9 9.2 - - - +
733B ALA* 3.8 36.8 - - + +
736B ILE* 3.9 13.4 - - + +
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Residues in contact with TYR 719 (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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781A PHE* 3.4 38.0 - + + -
782A ASN* 5.8 0.4 - - - -
785A SER* 2.4 29.7 + - - -
788A GLU* 5.2 0.7 + - - -
717B SER* 3.3 6.6 + - - +
718B ASP* 1.3 94.5 + - - +
720B GLY* 1.3 58.1 + - - +
722B ALA* 3.5 3.5 - - - +
723B GLN* 2.9 32.7 + - - +
729B ARG* 3.5 39.2 + - + -
1D A 3.3 51.4 - - - +
2D C 3.3 14.7 + - - -
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Residues in contact with GLY 720 (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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716B ILE* 3.7 8.4 - - - +
717B SER* 3.0 10.9 + - - -
718B ASP 3.0 0.6 - - - -
719B TYR* 1.3 78.4 - - - +
721B LEU* 1.3 64.3 + - - +
723B GLN* 3.7 3.1 + - - +
724B ASN* 3.0 22.7 + - - +
3F G 3.6 26.2 + - - -
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Residues in contact with LEU 721 (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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708B VAL* 3.9 31.0 - - + +
712B ILE* 5.3 1.8 - - + -
716B ILE* 3.6 14.9 - - + +
717B SER 2.9 15.1 + - - +
718B ASP 3.8 2.9 - - - +
720B GLY* 1.3 75.7 - - - +
722B ALA* 1.3 61.7 + - - +
724B ASN* 3.0 23.1 - - - +
725B LEU* 3.2 39.5 - - + +
732B ALA* 3.2 17.0 - - + +
735B PHE* 4.3 19.5 - - + -
736B ILE* 3.2 35.0 - - + -
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Residues in contact with ALA 722 (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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781A PHE* 3.2 23.6 - - + -
563B LYS* 4.0 0.2 + - - -
718B ASP 2.7 21.7 + - - +
719B TYR 3.5 3.6 - - - +
721B LEU* 1.3 71.3 - - - +
723B GLN* 1.3 60.0 + - - +
724B ASN 2.9 8.6 + - - -
725B LEU 3.2 7.6 + - - -
726B ASN* 3.4 14.2 + - - -
727B ILE* 3.1 29.6 + - - +
728B SER 3.7 1.6 - - - +
729B ARG* 3.9 3.6 - - - -
732B ALA* 3.3 11.4 - - + +
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Residues in contact with GLN 723 (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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779A ARG 5.2 1.9 - - - +
781A PHE* 3.3 31.1 - - + -
547B LEU* 4.1 19.9 + - - +
548B LYS* 4.3 25.6 - - + +
559B ASP* 3.1 34.3 + - - +
560B VAL* 4.4 6.8 - - - +
563B LYS* 2.6 49.8 + - - +
719B TYR 2.9 19.5 + - - +
720B GLY* 4.0 2.9 - - - +
722B ALA* 1.3 72.3 - - - +
724B ASN* 1.3 58.1 + - - +
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Residues in contact with ASN 724 (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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559B ASP* 6.0 1.7 - - - +
563B LYS* 4.5 1.2 + - - -
704B GLN* 5.0 8.8 + - - +
707B ALA* 4.8 19.6 + - - +
708B VAL* 5.0 7.3 - - - +
716B ILE* 4.0 19.4 - - - +
720B GLY 3.0 15.1 + - - +
721B LEU* 3.0 23.7 - - - +
723B GLN* 1.3 80.6 - - - +
725B LEU* 1.3 68.3 + - + +
3F G 5.2 4.4 + - - -
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Residues in contact with LEU 725 (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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563B LYS* 3.1 18.3 - - - -
689B ILE* 4.1 27.8 - - + -
704B GLN* 4.0 26.4 + - + +
708B VAL* 3.8 28.3 - - + -
721B LEU* 3.2 31.2 - - + +
722B ALA 3.2 2.7 + - - -
724B ASN* 1.3 81.0 - - + +
726B ASN* 1.3 68.0 + - - +
727B ILE* 3.0 38.8 - - + -
735B PHE* 6.5 0.2 - - + -
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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