Contacts of the helix formed by residues 698 - 708 (chain A) in PDB entry 1LVK
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 TYR 698 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A ILE 3.5 1.6 + - - -
697A ILE* 1.3 71.7 - - + +
699A ALA* 1.3 63.6 + - - +
701A PHE* 3.0 15.1 + - - +
702A VAL* 3.2 16.8 + - - +
719A SER* 3.6 22.0 - - - -
720A GLN* 3.3 39.6 - - + +
723A THR* 3.6 17.7 - - + -
739A PHE* 3.1 35.7 - + - +
740A GLY 2.4 48.5 + - - -
741A ILE 4.5 0.2 - - - -
742A THR* 3.1 36.6 + - - +
743A LYS 3.1 5.2 + - - -
744A ILE* 4.0 11.2 - - + -
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Residues in contact with ALA 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A ILE* 3.4 10.5 - - + +
698A TYR* 1.3 77.3 - - - +
700A ASP* 1.3 59.7 + - - +
702A VAL* 3.4 3.7 + - - +
703A LYS* 2.9 31.7 + - - +
714A ARG 4.9 1.4 - - - +
716A ALA 5.5 0.4 - - - +
719A SER* 3.5 21.6 - - - +
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Residues in contact with ASP 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A ILE* 4.0 10.4 - - + +
697A ILE* 2.8 43.5 + - - +
699A ALA* 1.3 74.8 - - - +
701A PHE* 1.3 67.2 + - - +
703A LYS* 3.4 14.9 + - - +
704A ARG* 3.4 11.6 + - - +
705A TYR* 5.4 0.3 - - - -
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Residues in contact with PHE 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A ILE* 3.8 15.8 - - + +
697A ILE 3.0 10.2 + - - +
698A TYR 3.0 7.8 + - - +
700A ASP* 1.3 76.3 - - - +
702A VAL* 1.3 59.8 + - + +
704A ARG 3.1 3.1 + - - -
705A TYR* 2.8 77.1 + + + +
723A THR* 3.2 28.9 - - + +
726A VAL* 4.0 22.0 - - + -
727A LEU* 3.7 31.4 - - + -
744A ILE* 4.3 10.1 - - + -
746A PHE* 4.2 23.1 - + - -
751A LEU* 4.4 3.6 - - + -
754A ILE* 4.4 13.0 - - + -
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Residues in contact with VAL 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A TYR 3.2 10.7 + - - +
699A ALA* 3.8 6.7 - - - +
701A PHE* 1.3 75.4 - - + +
703A LYS* 1.3 66.3 + - - +
705A TYR 4.9 0.4 - - - -
706A TYR* 2.8 33.7 + - + +
712A VAL* 3.4 30.1 - - + -
713A PRO 3.7 2.2 - - - +
714A ARG 3.2 18.8 - - - +
716A ALA* 4.7 3.8 - - + +
719A SER* 3.4 20.4 - - - +
722A ALA* 3.4 29.4 - - + -
723A THR* 3.6 11.0 - - - +
726A VAL* 5.5 1.8 - - + -
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Residues in contact with LYS 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 4.6 15.2 + - - -
699A ALA 2.9 19.7 + - - +
700A ASP* 3.9 8.5 - - - +
701A PHE 3.2 0.8 - - - -
702A VAL* 1.3 79.5 - - - +
704A ARG* 1.3 59.0 + - + +
706A TYR* 3.2 20.6 - - - -
714A ARG* 3.9 20.7 + - + +
715A ASP* 6.2 0.2 - - - -
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Residues in contact with ARG 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP 3.4 24.0 + - - -
24A LEU 4.6 0.2 + - - -
25A PHE* 3.6 33.7 + - + +
28A THR* 3.2 22.2 + - - +
84A LYS* 3.8 24.4 - - - +
700A ASP 3.4 6.7 + - - +
701A PHE 3.1 3.0 + - - +
703A LYS* 1.3 82.8 - - + +
705A TYR* 1.3 90.3 + - + +
706A TYR* 3.6 0.6 - - - -
707A ASP* 3.2 13.7 - - - +
755A GLU* 2.7 38.6 + - - -
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Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.8 12.6 - + - -
84A LYS* 4.6 7.4 - - - -
85A PHE* 5.3 0.5 - - - -
700A ASP 5.4 0.2 - - - -
701A PHE* 2.8 72.3 + + + +
702A VAL 4.7 0.2 - - - -
704A ARG* 1.3 99.9 - - + +
706A TYR* 1.3 65.9 + - - +
707A ASP* 3.2 4.9 - - - -
708A LEU* 2.9 43.2 + - + +
726A VAL* 3.8 9.1 - - + +
751A LEU* 3.6 19.7 - - + +
754A ILE* 3.7 17.3 - - + -
755A GLU* 2.8 31.9 + - - +
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Residues in contact with TYR 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 6.1 1.0 - - - +
702A VAL 2.8 15.3 + - - +
703A LYS 3.2 24.7 - - - -
704A ARG 4.9 0.2 - - - -
705A TYR* 1.3 76.0 - - - +
707A ASP* 1.3 93.4 + - + +
708A LEU 3.0 6.2 + - - -
709A ALA* 3.1 23.7 + - - +
712A VAL* 3.4 45.1 - - + +
713A PRO* 3.7 2.2 - - + -
714A ARG* 3.0 39.5 - - + +
726A VAL* 4.4 4.3 - - - -
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Residues in contact with ASP 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 4.2 11.6 - - - +
704A ARG 3.2 18.2 - - - +
705A TYR 4.0 1.6 - - - -
706A TYR* 1.3 107.9 + - + +
708A LEU* 1.4 75.1 + - - +
709A ALA 3.2 6.0 + - - -
712A VAL 5.2 0.7 - - - -
759A GLU* 3.1 36.3 - - + +
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Residues in contact with LEU 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.7 11.0 - - + -
705A TYR* 2.9 38.1 + - + +
707A ASP* 1.4 93.9 - - - +
709A ALA* 1.3 58.7 + - - +
710A PRO* 4.2 0.6 - - - +
726A VAL* 4.2 7.2 - - + -
729A HIS* 3.3 21.0 + - - -
730A LEU* 4.0 13.5 - - + +
754A ILE* 3.6 17.9 - - + +
757A ALA* 3.1 44.6 - - + +
758A ARG 3.4 21.7 - - - +
759A GLU* 3.8 4.4 - - - +
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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