Contacts of the strand formed by residues 683 - 688 (chain F) in PDB entry 6MZL
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 PHE 683 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636F HIS* 6.1 0.3 - - - -
677F PHE* 3.4 6.4 - - - +
678F SER* 2.9 31.3 + - - -
680F ASN* 5.2 7.9 - - - -
682F ARG* 1.3 125.7 + - + +
684F LEU* 1.3 68.2 + - - +
695F LEU* 4.6 9.2 - - + -
696F TRP 3.8 3.6 - - - +
697F ASP* 3.2 32.1 - - + -
719F PHE* 3.7 19.1 - + + -
724F GLU* 3.2 34.3 - - + -
742F LYS 4.5 6.7 - - - -
743F ALA* 5.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 684 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636F HIS* 6.3 1.8 - - + -
651F VAL* 5.2 2.2 - - + -
653F LEU* 5.3 4.0 - - + -
665F PHE* 3.6 28.9 - - + -
675F LEU* 4.6 7.2 - - + -
676F THR 3.5 5.4 - - - +
677F PHE* 3.6 33.4 - - + -
682F ARG 4.4 2.9 - - - +
683F PHE* 1.3 82.9 - - - +
685F ALA* 1.3 60.7 + - - +
686F THR* 4.5 12.8 - - + -
694F LEU 4.2 0.4 - - - -
695F LEU* 3.3 14.2 - - - +
696F TRP* 3.2 45.3 + - + +
697F ASP 4.4 0.9 - - - -
698F ILE* 4.3 26.2 - - + +
719F PHE* 3.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 685 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675F LEU* 3.4 3.1 - - - -
676F THR* 2.9 44.9 + - - +
684F LEU* 1.3 73.4 - - - +
686F THR* 1.3 63.2 + - - +
693F VAL* 3.9 10.8 - - + -
694F LEU 3.7 3.8 - - - -
695F LEU* 5.8 0.7 - - + -
717F LEU* 3.6 15.9 - - + +
719F PHE* 3.8 19.8 - - + -
726F LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 686 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651F VAL* 4.6 11.7 - - + -
668F HIS* 5.3 1.6 - - - +
672F ILE* 5.6 2.9 - - - -
674F SER 3.8 7.2 - - - -
675F LEU* 3.8 26.9 - - + -
684F LEU* 4.5 9.9 - - + -
685F ALA* 1.3 77.9 - - - +
687F GLY* 1.3 60.7 + - - +
688F ALA* 4.1 1.0 + - - +
692F ARG 3.5 3.1 - - - +
693F VAL* 3.3 4.0 - - - +
694F LEU* 3.0 33.2 + - - +
696F TRP* 3.0 38.5 + - + +
717F LEU* 4.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 687 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672F ILE* 3.7 5.2 - - - +
673F HIS 3.5 6.2 + - - -
674F SER* 3.3 29.1 + - - +
686F THR* 1.3 72.9 - - - +
688F ALA* 1.3 60.7 + - - +
692F ARG 3.6 6.1 - - - -
693F VAL* 4.0 3.4 - - - -
714F VAL* 3.8 28.3 - - - -
717F LEU* 3.4 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 688 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668F HIS* 3.6 43.3 - - + +
670F GLY 4.4 6.7 - - - +
671F PRO 4.2 5.8 - - - +
672F ILE* 4.6 6.1 - - + +
673F HIS* 4.5 5.8 - - - +
686F THR 5.1 0.2 - - - +
687F GLY* 1.3 74.4 - - - -
689F THR* 1.3 59.7 + - - +
690F ASP 3.1 7.9 - - - +
691F GLY* 3.0 20.0 + - - -
692F ARG 3.3 7.5 + - - +
714F VAL* 3.7 12.2 + - - +
----------------------------------------------------------
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