Contacts of the helix formed by residues 632 - 646 (chain B) in PDB entry 5FWP
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 HIS 632 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A LYS* 5.2 9.9 + - - -
585B VAL 3.1 8.5 + - - -
586B SER* 3.3 25.6 - - - -
587B SER 3.2 8.0 - - - -
588B PRO* 3.4 30.1 - - + +
629B ASN* 2.9 49.2 + - - +
630B PRO 4.1 0.7 - - - +
631B ASP* 1.3 81.4 - - + +
633B PRO* 1.3 63.2 - - + +
634B ILE* 4.0 6.5 - - + +
635B VAL* 3.1 12.5 + - + +
636B GLU* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 633 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A LYS* 5.3 10.5 - - - +
690A ILE* 3.5 32.8 - - + -
631B ASP 3.7 6.5 - - - +
632B HIS* 1.3 90.1 - - + +
634B ILE* 1.3 53.4 + - + +
636B GLU* 3.8 7.5 - - + +
637B THR* 2.5 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A TYR* 3.9 20.4 - - + +
684A ILE* 4.1 9.0 - - + -
685A LYS* 3.7 32.5 - - + -
688A LEU* 4.1 15.4 - - + +
690A ILE* 3.7 20.6 - - + -
588B PRO* 4.0 29.4 - - + -
632B HIS* 3.1 1.9 - - + -
633B PRO* 1.3 77.1 - - - +
635B VAL* 1.3 59.1 + - + +
637B THR* 3.2 2.6 + - - -
638B LEU* 2.9 37.4 + - + +
654B LEU* 5.0 0.4 - - + -
658B LEU* 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B PHE* 3.5 24.2 - - + -
563B LEU* 3.4 11.3 - - + +
567B MET* 5.4 1.8 - - + -
588B PRO* 3.4 31.2 - - + +
628B ILE* 3.5 24.2 - - + -
629B ASN 3.3 19.1 - - - +
630B PRO* 3.9 8.7 - - + -
632B HIS* 3.1 9.3 + - + +
634B ILE* 1.3 77.4 - - + +
636B GLU* 1.3 58.6 - - - +
638B LEU* 3.2 10.6 + - + -
639B ARG 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LYS* 3.4 20.2 + - - -
560B PHE* 3.6 10.1 - - + -
630B PRO 5.0 1.8 - - - +
631B ASP 6.0 0.4 - - - -
632B HIS 2.9 17.1 + - - +
633B PRO* 3.8 8.3 - - + +
635B VAL* 1.3 74.5 - - - +
637B THR* 1.3 64.5 + - - +
639B ARG* 2.8 41.6 + - - +
640B GLN* 2.9 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LEU* 4.1 29.3 + - + +
690A ILE* 3.7 12.6 - - - +
633B PRO* 2.5 30.1 + - - +
634B ILE* 3.4 7.2 - - - -
636B GLU* 1.3 72.7 - - - +
638B LEU* 1.3 52.9 + - + +
640B GLN* 3.0 15.4 + - + +
641B LYS* 2.7 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 638 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LEU* 5.6 1.3 - - + -
563B LEU* 3.4 20.4 - - + +
567B MET* 3.6 22.2 - - + -
634B ILE* 2.9 24.6 + - + +
635B VAL* 3.4 13.9 - - + +
636B GLU 3.2 0.2 - - - -
637B THR* 1.3 77.3 - - + +
639B ARG* 1.3 52.3 + - - +
641B LYS* 3.1 8.5 + - + +
642B ALA* 2.7 30.0 + - - +
651B VAL* 3.9 24.9 - - + +
654B LEU* 3.8 26.7 - - + -
655B VAL* 4.4 7.9 - - + -
658B LEU* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LYS* 3.2 51.1 + - - +
560B PHE* 3.7 24.7 - - + -
563B LEU* 3.5 16.7 - - + +
635B VAL 3.0 6.3 + - - -
636B GLU* 2.8 39.3 + - - +
638B LEU* 1.3 74.5 - - - +
640B GLN* 1.3 69.2 + - - +
642B ALA* 3.1 5.4 + - + +
643B GLU* 2.8 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 640 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B GLU* 2.9 48.1 + - - +
637B THR* 3.3 15.0 + - + +
639B ARG* 1.3 85.9 - - - +
641B LYS* 1.3 60.0 + - + +
643B GLU* 3.2 15.2 + - - +
644B ALA* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 641 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LEU* 5.1 10.8 - - + -
637B THR* 2.7 44.4 + - + +
638B LEU* 3.1 10.5 + - + +
640B GLN* 1.3 72.7 - - + +
642B ALA* 1.3 61.5 + - - +
644B ALA* 3.6 9.4 - - + +
645B ASP* 2.8 33.2 + - - +
648B ASP* 5.2 3.7 - - - +
651B VAL* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 642 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ASN* 6.1 0.4 - - + -
563B LEU* 4.0 17.0 - - + +
566B LEU* 3.8 23.6 - - + -
638B LEU 2.7 12.9 + - - +
639B ARG* 3.1 10.1 + - - +
641B LYS* 1.3 77.0 - - - +
643B GLU* 1.3 62.5 + - + +
645B ASP* 3.4 0.3 + - - -
646B LYS* 3.0 49.1 + - + +
651B VAL* 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 643 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B ARG* 2.8 51.8 + - + +
640B GLN* 3.2 17.2 + - - +
642B ALA* 1.3 78.3 - - + +
644B ALA* 1.3 61.8 + - - +
645B ASP* 4.6 0.2 - - - -
646B LYS* 5.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 644 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B GLN 2.8 16.9 + - - +
641B LYS* 3.6 14.6 - - + +
643B GLU* 1.3 78.5 - - - +
645B ASP* 1.3 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 645 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LYS 2.8 19.4 + - - +
642B ALA* 3.4 1.2 + - - -
643B GLU 4.6 0.2 - - - -
644B ALA* 1.3 79.8 - - + +
646B LYS* 1.3 63.9 + - - +
647B ASN* 2.8 31.9 + - - +
648B ASP* 3.0 38.5 + - + +
651B VAL* 5.1 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 646 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ASN* 3.7 40.9 + - - +
566B LEU* 3.3 45.7 - - + +
569B GLU* 5.9 0.9 - - - +
642B ALA* 3.0 41.8 + - + +
643B GLU* 5.7 1.3 - - - +
645B ASP* 1.3 71.6 + - - +
647B ASN* 1.3 64.5 + - - +
648B ASP 3.3 1.6 + - - +
651B VAL* 6.0 0.7 - - - +
652B LYS* 3.4 12.6 - - - +
----------------------------------------------------------
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