Contacts of the helix formed by residues 634 - 644 (chain E) in PDB entry 3LVQ
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 634 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E VAL* 3.0 18.2 - - + +
595E LYS 3.0 12.3 - - - +
597E ALA* 2.8 56.0 + - - +
598E ASN* 4.3 2.8 - - - +
629E ALA* 3.4 16.2 + - - +
632E TYR* 3.3 23.7 - - + +
633E ASN* 1.3 76.1 + - - +
635E PRO* 1.3 67.3 - - - +
636E ASP 3.7 0.9 - - - -
637E CYS* 3.3 26.7 - - + +
638E LEU* 3.0 20.4 - - - +
670E CYS* 4.5 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 635 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633E ASN* 3.1 19.1 - - - +
634E GLN* 1.3 82.4 - - - +
636E ASP* 1.3 68.9 + - + +
637E CYS 3.0 4.0 - - - -
638E LEU* 2.9 36.1 + - + +
639E LYS* 3.2 9.8 + - - +
669E GLU* 3.4 43.7 - - + +
670E CYS* 4.6 5.4 - - - +
673E LEU* 4.4 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 636 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599E GLN* 4.8 10.4 + - - +
602E LEU* 4.1 31.4 - - + +
635E PRO* 1.3 87.4 - - + +
637E CYS* 1.3 63.0 + - - +
639E LYS* 3.4 34.0 + - + +
640E LEU* 3.2 22.9 + - - +
669E GLU* 4.7 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 637 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E VAL* 4.0 27.1 - - + -
597E ALA* 3.9 27.8 - - - -
602E LEU* 4.3 13.9 - - - +
605E VAL* 4.4 12.9 - - + +
629E ALA* 4.4 0.9 - - + -
634E GLN* 3.3 30.6 + - + +
635E PRO 3.0 0.4 - - - -
636E ASP* 1.3 76.7 - - - +
638E LEU* 1.3 66.8 + - - +
640E LEU* 3.2 7.5 + - - +
641E LEU* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 638 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626E LEU* 4.4 16.2 - - + -
629E ALA* 3.6 28.3 - - + +
630E ALA* 5.1 3.6 - - + -
634E GLN 3.0 25.5 + - - +
635E PRO* 2.9 10.5 + - + +
637E CYS* 1.3 77.1 - - - +
639E LYS* 1.3 64.6 + - - +
641E LEU* 3.0 20.2 + - - +
642E LEU* 3.1 25.8 + - + +
670E CYS* 3.7 31.6 - - + +
673E LEU* 4.8 11.7 - - + -
674E LEU* 4.0 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 639 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635E PRO 3.2 10.0 + - - +
636E ASP* 3.4 39.2 + - - +
638E LEU* 1.3 78.3 - - - +
640E LEU* 1.3 62.9 + - + +
642E LEU* 3.5 6.1 + - - +
643E LYS* 3.1 22.3 + - - +
669E GLU* 5.2 6.4 + - - -
673E LEU* 4.1 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 640 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489E SER* 4.1 21.3 - - - +
492E LEU* 4.2 18.4 - - + -
602E LEU* 4.0 29.4 - - + +
605E VAL* 4.5 4.5 - - + -
606E ASP* 4.0 37.9 - - + +
609E ILE* 3.9 19.1 - - + +
636E ASP 3.2 5.5 + - - +
637E CYS* 3.2 9.6 + - - +
639E LYS* 1.3 78.4 - - + +
641E LEU* 1.3 61.2 + - - +
643E LYS* 3.5 20.4 - - + +
644E GLY* 3.5 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 641 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590E LEU* 4.5 5.2 - - + -
594E VAL* 4.6 13.9 - - + -
605E VAL* 5.5 1.6 - - + -
609E ILE* 4.3 15.7 - - + -
615E LEU* 3.8 26.0 - - + +
625E ALA* 4.0 29.2 - - + +
626E LEU* 3.8 22.4 - - + +
629E ALA* 3.8 27.8 - - + -
637E CYS* 3.0 20.2 + - - +
638E LEU* 3.0 9.1 + - - +
640E LEU* 1.3 77.4 - - - +
642E LEU* 1.3 61.6 + - - +
644E GLY* 3.2 14.4 + - - -
646E ALA* 3.3 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 642 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626E LEU* 4.3 18.4 - - + -
638E LEU* 3.1 30.5 + - + +
639E LYS* 4.1 4.5 - - - +
641E LEU* 1.3 71.4 - - - +
643E LYS* 1.3 57.8 + - - +
644E GLY 3.0 2.0 - - - -
645E ARG* 2.8 25.8 + - - -
646E ALA 3.8 13.2 + - - +
648E VAL* 4.2 17.9 - - + -
673E LEU* 4.6 17.5 - - + +
674E LEU* 5.8 2.2 - - + -
677E ALA* 4.0 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 643 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ASP* 6.0 1.7 - - - +
489E SER* 3.2 48.3 + - - +
490E GLU* 3.7 21.3 - - - +
610E GLN* 5.2 11.4 - - - +
639E LYS 3.1 18.7 + - - +
640E LEU* 3.5 22.6 - - + +
642E LEU* 1.3 75.7 - - - +
644E GLY* 1.3 56.6 + - - +
645E ARG* 3.4 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 644 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ASP* 4.5 8.7 - - - +
609E ILE* 4.9 13.7 - - - +
615E LEU* 3.2 15.8 - - - +
640E LEU 3.5 5.8 + - - -
641E LEU 3.2 10.9 + - - -
642E LEU 3.0 1.0 - - - -
643E LYS* 1.3 78.0 - - - +
645E ARG* 1.3 78.5 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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