Contacts of the helix formed by residues 698 - 714 (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 THR 698 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B GLU 2.8 9.3 + - - -
697B VAL* 1.3 82.8 - - - +
699B PRO* 1.3 83.2 - - + +
700B ASN* 3.1 26.5 - - + +
701B MET* 3.1 39.1 + - - +
702B ARG* 3.4 2.9 + - - +
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Residues in contact with PRO 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B VAL 4.6 0.4 - - - +
698B THR* 1.3 92.6 - - + +
700B ASN* 1.3 62.7 + - + +
702B ARG* 3.5 6.0 + - + +
703B ARG* 3.2 29.1 + - - +
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Residues in contact with ASN 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ARG* 4.6 21.3 + - + +
698B THR* 3.1 14.5 - - + +
699B PRO* 1.3 80.1 - - + +
701B MET* 1.3 55.8 + - - +
703B ARG* 4.4 9.6 + - - +
704B GLN* 2.7 56.5 + - - +
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Residues in contact with MET 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B ALA* 3.4 5.5 - - + +
690B PHE* 3.3 44.7 - - + -
692B VAL* 3.7 28.0 - - + -
696B GLU* 3.4 10.5 - - + +
697B VAL* 3.6 17.3 - - + -
698B THR* 3.1 51.7 + - - +
700B ASN* 1.3 78.0 - - - +
702B ARG* 1.3 56.9 + - - +
704B GLN 3.3 0.2 + - - -
705B ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B DCP 2.8 45.8 + - - -
655B SER* 5.4 0.4 + - - -
656B GLN* 4.5 1.2 - - - +
680B ASP* 3.0 24.7 + - - -
682B HIS* 4.2 15.8 - - + +
683B THR* 3.4 31.6 - - + +
686B ALA* 4.0 9.4 - - - -
697B VAL* 4.0 8.9 - - + +
698B THR 3.4 7.7 + - - +
699B PRO* 3.9 8.7 - - + +
700B ASN 3.3 0.2 - - - -
701B MET* 1.3 75.8 - - - +
703B ARG* 1.3 62.9 + - + +
705B ALA* 2.8 18.9 + - - +
706B LYS* 2.9 28.0 + - - +
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Residues in contact with ARG 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B ILE* 4.7 7.7 - - - +
629B ARG* 4.1 47.9 - - - +
699B PRO* 3.2 21.2 + - - +
700B ASN* 3.8 9.3 + - - +
702B ARG* 1.3 79.7 - - + +
704B GLN* 1.3 57.6 + - - +
706B LYS* 3.1 44.9 + - - +
707B ALA* 3.5 7.3 + - - +
28E G 4.6 10.1 + - - -
29E A 3.1 28.9 + - - -
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Residues in contact with GLN 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B PHE* 3.7 31.9 - - + -
700B ASN* 2.7 42.5 + - - +
701B MET 3.7 3.6 - - - +
703B ARG* 1.3 73.4 - - - +
705B ALA* 1.3 58.5 + - - +
707B ALA* 4.0 7.2 + - + +
708B VAL* 3.1 26.7 + - + +
724B ASN* 5.0 8.6 + - - +
725B LEU* 4.0 31.8 - - + +
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Residues in contact with ALA 705 (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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682B HIS 3.2 26.7 - - - +
685B THR* 3.8 9.2 - - + -
686B ALA* 3.4 19.7 - - + +
689B ILE* 5.9 0.9 - - - -
690B PHE* 5.2 1.8 - - + -
701B MET 2.9 12.8 + - - +
702B ARG 2.8 10.2 + - - +
704B GLN* 1.3 76.9 - - - +
706B LYS* 1.3 64.2 + - - +
708B VAL* 3.0 6.3 + - - +
709B ASN* 3.0 28.1 + - - -
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Residues in contact with LYS 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B DCP 3.1 66.7 + - + +
682B HIS* 3.9 19.7 - - + +
702B ARG* 2.9 26.8 + - - +
703B ARG* 3.1 36.3 - - + +
705B ALA* 1.3 77.6 - - - +
707B ALA* 1.3 61.9 + - - +
708B VAL 3.2 0.9 + - - -
709B ASN* 3.3 8.8 + - - +
710B PHE* 3.2 42.1 + - + -
29E A 5.6 4.7 + - - +
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Residues in contact with ALA 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B DCP 4.1 11.4 + - - +
703B ARG 3.5 6.0 + - - +
704B GLN* 4.3 8.7 - - + +
705B ALA 3.3 0.4 - - - -
706B LYS* 1.3 78.6 - - - +
708B VAL* 1.3 59.2 + - + +
710B PHE* 5.2 0.2 - - - -
711B GLY* 2.9 27.9 + - - +
724B ASN* 4.8 16.0 + - - +
3F G 4.0 23.2 - - - +
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Residues in contact with VAL 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B THR* 4.2 8.5 - - + -
689B ILE* 4.8 7.2 - - + -
704B GLN* 3.1 20.0 - - + +
705B ALA* 3.0 11.5 + - - +
707B ALA* 1.3 77.8 - - + +
709B ASN* 1.3 60.6 + - - +
711B GLY* 4.9 0.2 - - - -
712B ILE* 2.9 32.6 + - + +
716B ILE* 6.5 0.2 - - - -
721B LEU* 3.9 24.6 - - + +
724B ASN* 5.0 8.5 - - - +
725B LEU* 3.8 25.4 - - + -
735B PHE* 4.0 26.2 - - + -
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Residues in contact with ASN 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B LEU* 4.6 6.5 - - + -
681B ILE* 3.5 5.3 + - - +
682B HIS* 2.5 56.5 + - + +
685B THR* 2.5 29.7 + - - +
705B ALA 3.0 13.0 + - - +
706B LYS 3.3 2.6 + - - +
708B VAL* 1.3 74.4 - - - +
710B PHE* 1.3 61.5 + - - +
712B ILE* 2.9 18.9 - - - +
713B VAL* 2.9 19.7 + - - +
739B TYR* 2.5 28.5 + - - +
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Residues in contact with PHE 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B DCP 2.9 76.9 - + + +
658B GLU* 3.8 9.9 - - + -
659B LEU* 3.5 29.2 - - + -
682B HIS* 3.5 19.3 - + - -
706B LYS* 3.2 29.7 + - + +
707B ALA 4.7 0.2 - - - +
709B ASN* 1.3 73.6 - - - +
711B GLY* 1.3 68.1 + - - +
713B VAL* 3.8 5.8 - - + -
714B TYR* 2.9 44.5 + + + +
3F G 3.7 22.4 - - + +
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Residues in contact with GLY 711 (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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707B ALA 2.9 22.7 + - - -
708B VAL* 4.0 0.9 - - - -
710B PHE* 1.3 79.7 - - - +
712B ILE* 1.3 57.2 + - - +
714B TYR 3.7 1.2 + - - -
716B ILE* 2.9 35.9 + - - +
3F G 3.3 33.6 + - - -
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Residues in contact with ILE 712 (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* 2.9 27.6 + - + +
709B ASN 2.9 16.4 - - - +
711B GLY* 1.3 75.6 - - - +
713B VAL* 1.3 60.9 + - - +
714B TYR 3.1 2.5 + - - -
715B GLY* 3.6 8.7 + - - -
716B ILE* 3.5 13.8 + - + +
721B LEU* 5.3 2.2 - - + -
735B PHE* 5.1 2.2 - - + -
736B ILE* 3.4 36.1 - - + +
739B TYR* 3.1 62.4 - - + -
740B PHE* 3.0 28.7 - - + -
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Residues in contact with VAL 713 (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* 4.8 8.3 - - + -
662B LEU* 4.0 17.3 - - + -
709B ASN 2.9 18.4 + - - +
710B PHE* 3.5 19.7 - - + +
712B ILE* 1.3 76.8 - - - +
714B TYR* 1.3 81.5 + - + +
715B GLY 3.4 3.1 + - - -
739B TYR* 3.9 21.5 - - + +
740B PHE* 4.3 2.9 - - + -
746B VAL* 3.8 28.9 - - + -
750B MET* 3.0 33.6 - - - +
792B MET* 4.6 0.3 - - - +
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Residues in contact with TYR 714 (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* 2.5 30.2 + - - +
662B LEU* 5.9 0.7 - - + -
710B PHE* 2.9 37.8 + + + +
711B GLY 3.8 1.6 - - - -
712B ILE 3.1 0.2 - - - -
713B VAL* 1.3 92.8 - - + +
715B GLY* 1.3 56.4 + - - +
716B ILE 3.8 1.1 - - - -
750B MET* 4.4 2.0 - - + -
789B ARG* 3.9 5.9 - - - +
792B MET* 3.2 17.6 - - - +
793B ASN* 3.2 52.2 + - + +
796B ILE* 3.2 34.2 - - + +
3F G 2.9 57.6 - - + +
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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