Contacts of the helix formed by residues 644 - 652 (chain A) in PDB entry 4REA
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 644 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ASP* 4.1 13.2 + - - -
600A ASP* 5.0 1.0 - - - +
604A ARG* 2.5 40.6 + - - +
641A LEU* 2.9 17.6 + - + +
642A LYS 3.2 0.9 - - - +
643A ASN* 1.3 80.9 - - - +
645A PRO* 1.3 84.6 - - + +
646A SER* 2.3 64.0 + - - -
647A LEU* 3.2 21.0 + - + +
648A ARG* 4.3 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLN* 5.2 0.3 - - - +
643A ASN 3.9 4.5 - - - +
644A HIS* 1.3 102.8 - - + +
646A SER* 1.3 60.6 + - - +
647A LEU 3.1 1.1 + - - -
648A ARG* 3.4 25.3 + - + +
649A CYS* 4.0 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLN* 3.8 25.2 - - - +
601A ASP* 3.2 26.9 + - - -
604A ARG* 2.9 10.7 + - - -
644A HIS* 2.3 53.1 + - - +
645A PRO* 1.3 74.7 - - - +
647A LEU* 1.3 62.6 + - - +
649A CYS 3.3 3.1 + - - -
650A HIS* 3.3 27.9 + - - -
662A VAL* 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TRP* 3.6 23.3 - - + -
641A LEU 3.6 8.3 - - - +
642A LYS* 2.8 45.3 - - + +
644A HIS* 3.6 8.7 - - + +
645A PRO 3.1 0.6 - - - -
646A SER* 1.3 80.3 + - - +
648A ARG* 1.3 66.1 + - + +
650A HIS* 3.0 20.9 + - - +
651A GLU* 3.0 37.0 + - - +
662A VAL* 3.8 15.5 - - + -
663A GLY 4.2 0.4 - - - +
699A TYR* 3.6 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ASN 5.9 0.7 - - - +
644A HIS 4.5 5.2 - - - +
645A PRO* 3.5 19.7 - - + +
646A SER 3.2 0.4 - - - -
647A LEU* 1.3 78.0 - - + +
649A CYS* 1.3 54.5 + - - +
651A GLU* 3.4 23.3 + - - +
652A ASP* 2.6 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A HIS* 4.6 14.6 - - - -
597A GLN* 3.4 47.8 - - + +
645A PRO 4.0 2.1 + - - +
646A SER 3.3 2.6 + - - +
647A LEU 3.1 0.6 - - - -
648A ARG* 1.3 75.8 - - - +
650A HIS* 1.3 66.8 + - - +
652A ASP* 3.2 23.7 + - - +
653A LEU* 3.6 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A ILE 3.9 15.8 + - - -
596A PHE* 4.4 1.6 - - - -
597A GLN* 4.6 3.4 - - - -
601A ASP* 2.6 42.1 + - - -
646A SER* 3.3 17.2 + - - -
647A LEU* 3.0 25.4 + - + +
649A CYS* 1.3 78.5 - - - +
651A GLU* 1.3 60.9 + - - +
653A LEU* 3.1 21.1 + - + +
658A ARG* 3.2 21.0 - - + +
661A THR* 3.6 36.7 - - + +
662A VAL* 3.6 19.2 - - + +
699A TYR* 4.5 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TRP* 5.8 0.2 - - - -
647A LEU* 3.0 36.2 + - - +
648A ARG* 3.8 18.4 + - - +
649A CYS 3.3 0.4 - - - -
650A HIS* 1.3 75.9 - - - +
652A ASP* 1.3 57.6 + - - +
653A LEU 4.0 0.2 - - - +
658A ARG* 2.6 23.1 + - - +
698A ILE* 3.3 46.8 - - + +
699A TYR* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ARG* 2.6 36.3 + - - +
649A CYS* 3.4 16.9 - - - +
650A HIS 3.1 0.6 - - - -
651A GLU* 1.3 76.6 - - - +
653A LEU* 1.3 65.4 + - + +
654A PRO* 3.7 4.2 - - - +
----------------------------------------------------------
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