Contacts of the strand formed by residues 650 - 655 (chain A) in PDB entry 6F3T
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 THR 650 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A SER* 3.5 29.6 - - - +
360A ALA* 5.0 8.3 - - + -
626A HIS* 3.2 19.3 + - - -
646A SER 3.3 23.4 + - - -
648A ASP* 2.8 26.3 + - + +
649A ARG* 1.3 79.1 - - - +
651A VAL* 1.3 62.8 + - - +
652A ARG* 3.5 15.8 + - - +
664A ILE* 4.5 9.0 - - + -
665A PHE 3.6 8.3 - - - -
666A THR* 4.0 10.5 - - + -
672A ILE* 3.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ALA* 5.0 0.2 - - + -
644A THR 3.3 13.2 - - - +
645A GLY* 4.5 0.2 - - - -
650A THR* 1.3 78.1 - - - +
652A ARG* 1.3 68.5 + - - +
664A ILE* 3.5 2.3 - - - +
665A PHE* 2.6 57.0 + - + +
668A HIS* 4.6 2.9 - - + -
672A ILE* 3.9 24.0 - - + -
675A LEU* 4.1 6.5 - - + -
684A LEU* 3.9 28.3 - - + -
686A THR* 3.8 30.1 - - + +
696A TRP* 5.0 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ALA* 4.7 11.1 - - - +
625A GLY* 3.6 34.8 + - - -
626A HIS* 3.5 20.4 - - + -
627A LEU* 3.9 17.8 - - - +
643A ALA* 3.1 6.2 - - - +
644A THR* 2.8 34.7 + - - +
648A ASP* 4.0 6.7 + - - -
650A THR* 3.5 17.2 + - - +
651A VAL* 1.3 81.7 - - - +
653A LEU* 1.3 59.3 + - - +
654A TRP* 3.6 31.0 - - + +
661A CYS* 3.9 13.8 - - - +
663A ARG 3.3 10.8 - - - +
664A ILE* 4.2 26.3 - - + +
665A PHE* 5.7 1.1 - - - -
684A LEU* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A VAL* 4.1 9.9 - - + -
636A HIS* 6.0 0.9 - - + -
641A TYR* 4.1 16.2 - - + -
642A VAL 3.3 13.7 - - - +
643A ALA* 3.9 6.1 - - + -
652A ARG* 1.3 73.4 - - - +
654A TRP* 1.3 60.9 + - - +
661A CYS* 3.6 3.6 - - - -
662A VAL* 2.8 42.5 + - + -
663A ARG* 3.1 29.7 + - + +
665A PHE* 5.1 4.9 - - + -
677A PHE* 3.8 32.5 - - + -
684A LEU* 5.3 4.5 - - + -
698A ILE* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A PHE* 3.4 43.3 - + + -
624A ALA 3.4 42.0 - - - -
625A GLY* 4.0 6.5 - - - -
626A HIS* 4.1 13.5 - + - -
641A TYR* 3.2 13.2 - - - -
642A VAL* 2.6 45.6 + - + +
644A THR* 2.9 31.4 + - + +
652A ARG* 3.6 34.7 - - + +
653A LEU* 1.3 76.3 - - - +
655A ASP* 1.3 60.8 + - - +
659A GLY 3.6 20.9 - - - -
660A ASN 3.3 4.7 - - - +
661A CYS* 3.8 26.7 - - + -
662A VAL* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 2.6 39.6 + - - -
623A PHE* 3.9 2.4 - - - -
640A ASN 3.4 2.1 - - - +
641A TYR* 3.8 20.1 + - + -
654A TRP* 1.3 70.3 - - - +
656A VAL* 1.3 61.8 + - - +
657A LEU* 3.0 12.3 + - - -
658A ASN* 3.4 26.0 + - - +
659A GLY* 2.7 35.3 + - - -
660A ASN* 2.8 14.1 + - + +
662A VAL* 4.0 12.4 - - + +
----------------------------------------------------------
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