Contacts of the helix formed by residues 637 - 643 (chain B) in PDB entry 5N4D
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 PRO 637 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B ARG* 3.4 19.8 + - - +
633B ASP 3.3 25.1 - - - +
634B TYR* 3.8 9.4 - - - +
635B ILE 3.6 1.6 - - - -
636B TYR* 1.3 94.3 - - + +
638B LEU* 1.3 57.8 + - + +
643B ASN* 3.3 24.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
543B ARG 5.6 0.7 - - - +
546B LYS* 3.7 37.2 - - + -
547B VAL* 3.8 30.3 - - + +
550B PHE* 3.8 18.5 - - + -
585B GLY* 5.1 4.9 - - - -
589B ARG* 3.5 33.5 - - - +
607B LEU* 4.1 13.4 - - + +
634B TYR* 4.0 13.5 - - + +
635B ILE* 2.9 9.9 + - - +
637B PRO* 1.3 80.1 - - + +
639B SER* 1.3 65.5 + - - +
640B PRO* 3.2 11.4 - - - +
643B ASN* 4.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ALA 3.4 3.3 + - - -
607B LEU* 3.0 37.5 + - - -
608B LEU* 4.6 2.5 - - - -
635B ILE 3.1 6.9 + - - -
636B TYR* 3.3 14.3 + - - -
638B LEU* 1.3 74.9 - - - +
640B PRO* 1.3 69.4 - - - +
642B HIS* 2.7 35.5 + - - -
643B ASN* 2.8 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 640 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LEU* 3.6 31.2 - - + -
584B MET* 4.1 13.9 - - + +
585B GLY* 3.7 21.3 - - - +
588B VAL* 4.1 6.6 - - + +
605B ALA* 3.2 19.3 - - + +
607B LEU* 4.4 2.5 - - + -
638B LEU 3.2 8.1 - - - +
639B SER* 1.3 82.2 - - - +
641B VAL* 1.3 62.6 + - - +
642B HIS 3.0 1.2 + - - -
643B ASN* 3.1 13.6 + - + +
644B VAL* 3.5 16.5 + - - +
672B PHE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 641 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 5.0 4.3 - - - +
605B ALA* 3.0 38.5 + - + +
606B ASP* 3.8 10.5 - - + +
639B SER 3.3 0.2 - - - -
640B PRO* 1.3 75.2 - - - +
642B HIS* 1.3 77.8 + - + +
643B ASN 3.7 0.3 + - - -
644B VAL* 4.4 1.5 + - - +
668B HIS 4.3 0.7 - - - +
671B LYS* 4.1 22.7 - - + -
672B PHE* 4.0 26.7 - - - +
675B THR* 3.7 32.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 642 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.6 27.1 - - + +
34B PRO 5.0 4.3 - - - -
35B ASP* 4.7 8.8 + - - -
606B ASP* 3.3 29.6 + - - -
608B LEU* 3.3 28.2 - - + +
636B TYR* 3.9 19.5 + + + +
639B SER* 2.7 32.1 + - - +
641B VAL* 1.3 91.1 - - + +
643B ASN* 1.3 69.3 + - - +
644B VAL 3.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 643 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B VAL* 2.9 32.3 - - + +
589B ARG* 6.1 0.9 - - + -
636B TYR 2.9 24.9 + - - -
637B PRO* 3.3 26.9 + - - +
638B LEU 5.4 0.9 - - - -
639B SER 2.8 23.8 + - - +
640B PRO* 3.1 3.1 + - + -
642B HIS* 1.3 84.9 + - - +
644B VAL* 1.3 64.0 + - - +
645B ARG* 3.4 11.9 + - - +
----------------------------------------------------------
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