Contacts of the helix formed by residues 631 - 643 (chain F) in PDB entry 5LS6
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 631 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594D TRP* 3.1 75.4 - - + +
625F GLY 4.7 2.6 + - - +
626F PHE* 3.7 29.7 - - + +
627F ILE* 3.3 25.3 - - - +
628F ALA* 3.6 16.0 - - + +
629F ASP 3.1 0.4 - - - -
630F ASN* 1.3 78.7 - - - +
632F MET* 1.3 49.2 + - - +
633F ASN 3.1 2.3 + - - -
634F HIS* 3.1 11.9 + - - +
635F ALA* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 632 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D PHE* 3.7 35.4 - - + -
617F TRP* 3.9 13.2 - - + -
621F VAL* 4.8 0.2 - - + -
626F PHE* 3.6 31.0 - - + -
628F ALA 4.2 1.6 - - - +
629F ASP 2.9 18.4 + - - +
631F GLN* 1.3 73.0 - - - +
633F ASN* 1.3 59.6 + - - +
635F ALA* 3.6 19.2 - - + -
636F CYS* 3.2 22.3 + - - -
663F MET* 3.5 22.2 - - + -
668F LEU* 4.0 23.3 - - + +
669F ILE* 3.2 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 633 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630F ASN* 3.9 14.6 + - - +
631F GLN 3.1 1.2 + - - -
632F MET* 1.3 73.1 - - - +
634F HIS* 1.3 68.5 + - - +
636F CYS* 2.9 15.3 + - - +
637F MET* 3.0 22.3 + - - +
668F LEU 4.2 10.4 - - - +
669F ILE* 4.0 5.9 - - - +
670F SER* 3.6 24.3 + - - +
673F SER* 2.6 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 634 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626F PHE* 5.0 5.1 - - - -
630F ASN 4.7 1.3 + - - +
631F GLN* 3.1 12.7 + - + +
633F ASN* 1.3 78.8 - - - +
635F ALA* 1.3 57.9 + - - +
637F MET* 3.5 23.1 + - + +
638F LEU* 3.0 57.3 + - + +
322G PRO* 4.1 22.2 - - + +
323G GLN* 3.6 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 635 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617F TRP* 3.5 9.9 - - + -
620F HIS* 3.1 25.3 + - - -
626F PHE* 3.3 38.6 - - + -
631F GLN 2.8 17.9 + - - +
632F MET* 3.6 27.8 - - + +
633F ASN 3.1 0.4 - - - -
634F HIS* 1.3 72.9 + - - +
636F CYS* 1.3 60.6 + - - +
638F LEU 4.1 0.9 - - - -
639F PHE 3.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 636 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617F TRP* 3.9 23.1 - - - -
632F MET 3.2 23.9 + - - +
633F ASN* 2.9 5.5 + - - +
635F ALA* 1.3 74.9 - - - +
637F MET* 1.3 65.4 + - + +
639F PHE* 3.3 15.6 + - - +
640F VAL* 3.5 13.7 + - - +
656F PHE* 4.5 2.9 - - - -
659F HIS* 4.6 2.5 - - - -
660F LEU* 3.7 31.4 - - + -
663F MET* 4.0 8.7 - - - -
669F ILE* 3.9 17.5 - - + -
673F SER* 5.5 4.7 - - - -
677F ALA* 4.8 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 637 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633F ASN* 3.0 25.1 + - - +
634F HIS* 3.8 20.9 - - + +
636F CYS* 1.3 77.8 - - + +
638F LEU* 1.3 61.3 + - - +
640F VAL* 3.1 25.6 - - - +
641F GLU* 3.2 26.2 + - - +
673F SER* 5.8 6.1 - - - +
676F LYS* 3.8 40.6 - - + +
677F ALA* 5.3 9.4 - - + +
680F LYS* 4.4 11.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 638 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620F HIS* 3.5 16.2 - - + +
624F HIS* 3.7 34.8 - - + +
626F PHE* 4.6 5.8 - - + -
634F HIS* 3.0 45.3 + - + +
637F MET* 1.3 74.5 - - - +
639F PHE* 1.3 61.0 + - - +
641F GLU* 3.6 23.2 - - + +
642F ASN* 2.8 45.8 + - - +
322G PRO* 5.1 6.3 - - + -
323G GLN* 6.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 639 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613F VAL* 4.3 11.7 - - + -
616F LEU* 3.5 17.7 - - + -
617F TRP* 3.4 54.3 - + + -
620F HIS* 3.5 22.6 - + + +
635F ALA 3.5 12.9 + - - +
636F CYS 3.3 10.2 + - - +
637F MET 3.3 0.8 - - - -
638F LEU* 1.3 78.3 - - - +
640F VAL* 1.3 55.7 + - - +
643F TYR* 2.8 37.5 + + + +
644F GLY 3.1 5.4 + - - -
647F ILE* 3.3 30.3 - - + -
656F PHE* 3.4 32.3 - + - -
659F HIS* 5.4 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 640 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636F CYS 3.5 5.4 + - - +
637F MET* 3.1 18.5 + - - +
638F LEU 3.2 0.6 - - - -
639F PHE* 1.3 74.6 - - - +
641F GLU* 1.3 68.5 + - - +
642F ASN 3.2 2.6 - - - +
644F GLY* 3.2 25.4 + - - +
647F ILE* 5.9 0.2 - - + -
656F PHE* 3.3 40.6 - - + -
677F ALA* 4.1 13.0 - - + +
680F LYS* 3.9 35.2 - - + +
681F LEU* 4.4 14.1 - - + +
684F MET* 3.6 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 641 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637F MET* 3.2 27.3 + - - +
638F LEU* 3.2 24.8 + - + +
640F VAL* 1.3 81.2 - - - +
642F ASN* 1.3 70.0 + - - +
680F LYS* 3.0 36.2 + - - +
684F MET* 4.4 11.9 - - + +
428G GLU* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 642 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620F HIS* 4.2 2.6 + - - -
623F LYS* 5.6 2.1 - - - +
624F HIS* 3.8 24.9 + - - -
638F LEU* 2.8 30.2 + - - +
640F VAL 3.8 0.2 - - - +
641F GLU* 1.3 83.7 + - - +
643F TYR* 1.3 83.1 + - + +
644F GLY 3.2 3.0 + - - -
645F GLN* 3.7 16.6 + - - +
646F LYS* 5.7 0.5 - - - +
684F MET* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 643 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616F LEU* 3.4 50.5 - - + -
619F LEU* 3.8 24.7 + - + +
620F HIS* 3.7 24.5 - + + -
623F LYS* 4.2 19.3 - - + +
639F PHE* 2.8 43.7 + + + +
642F ASN* 1.3 87.1 - - + +
644F GLY* 1.3 54.9 + - - -
645F GLN 3.1 3.1 - - - -
646F LYS* 2.9 26.1 + - - +
647F ILE* 2.9 28.6 + - + +
----------------------------------------------------------
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