Contacts of the strand formed by residues 607 - 611 (chain D) in PDB entry 4Z2C
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 MET 607 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 3.3 16.8 - - - +
5A ASN 3.7 6.1 + - - -
6A LEU* 3.5 18.6 - - + -
7A VAL* 2.9 30.7 + - - +
430D PHE* 3.7 11.4 - - + -
502D VAL* 3.7 42.2 - - + -
536D TYR* 3.9 23.8 - - + -
537D ILE 3.7 2.5 - - - +
538D ALA* 4.1 11.0 - - + -
539D GLN* 4.2 2.9 - - - -
599D THR 4.4 3.4 - - - +
605D ARG* 3.4 37.9 + - + +
606D LEU* 1.3 78.8 - - - +
608D ALA* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 608 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.7 9.0 - - + -
8A ASN 5.0 0.4 - - - -
9A VAL* 3.8 24.0 - - + +
536D TYR* 3.3 9.1 - - - -
537D ILE* 2.9 45.0 + - + +
539D GLN* 3.3 24.6 - - - +
607D MET* 1.3 72.9 - - - +
609D ARG* 1.3 60.8 + - - +
610D VAL 3.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 609 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLN* 4.7 7.9 + - - +
6A LEU* 4.7 12.8 - - + +
7A VAL 3.0 17.9 + - - +
8A ASN* 3.5 17.3 - - + +
9A VAL 2.9 24.2 + - - -
532D ALA 5.2 0.2 + - - -
533D GLY* 2.6 43.2 + - - -
535D VAL 4.6 1.1 - - - -
536D TYR* 2.5 48.9 + - + -
607D MET 4.0 0.6 + - - -
608D ALA* 1.3 70.7 - - - +
610D VAL* 1.3 63.7 + - - +
611D SER* 3.0 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 610 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.4 10.1 - - - -
11A LEU* 5.2 12.3 - - + +
519D LEU* 5.0 10.5 - - + -
530D LEU* 4.0 19.2 - - + +
533D GLY* 5.1 4.0 - - - -
535D VAL* 3.2 40.0 + - + +
537D ILE* 5.3 9.6 - - + -
608D ALA 3.5 3.8 + - - +
609D ARG* 1.3 73.4 - - - +
611D SER* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 611 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 3.6 33.9 - - - -
9A VAL 2.7 9.7 + - - -
10A ASN* 3.3 7.2 - - - +
11A LEU* 3.1 24.4 + - - -
530D LEU 5.6 0.2 - - - -
609D ARG* 3.0 3.7 + - - -
610D VAL* 1.3 74.4 - - - +
612D VAL* 1.3 61.6 + - - +
613D ASP 4.0 1.2 + - - -
----------------------------------------------------------
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