Contacts of the strand formed by residues 643 - 647 (chain A) in PDB entry 2YA6
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 VAL 643 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LEU* 3.9 28.0 - - + -
571A LEU* 4.0 10.1 - - + -
635A VAL* 3.5 29.8 - - + -
636A VAL 3.5 4.0 - - - +
637A GLN* 4.3 3.1 - - + -
641A GLY 4.2 4.9 - - - +
642A ASP* 1.3 76.7 - - - +
644A LYS* 1.3 63.4 + - - +
657A ALA 3.7 0.7 - - - +
658A THR* 3.2 7.6 - - - +
659A SER* 2.8 42.2 + - - +
662A GLY* 4.2 19.5 - - - -
663A GLY* 4.8 0.7 - - - -
666A TRP* 3.9 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A THR 3.8 0.7 - - - +
635A VAL* 3.4 6.8 - - - +
636A VAL* 2.8 36.5 + - + +
638A LEU* 3.8 33.4 - - + -
642A ASP* 5.2 0.6 + - - -
643A VAL* 1.3 76.8 - - - +
645A LEU* 1.3 58.3 - - - +
646A PHE* 3.7 27.6 - - + -
656A VAL* 3.9 15.8 - - + +
657A ALA 3.4 1.3 - - - -
658A THR* 2.9 35.4 + - - +
671A LYS* 6.4 0.4 - - - +
673A TYR* 5.3 3.8 + - - -
696A ILE* 4.7 1.6 - - + -
720A GLY* 3.0 30.6 + - - -
721A GLU* 4.9 2.2 - - - +
722A LEU* 4.9 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A PRO* 4.8 0.9 - - + -
589A SER* 3.9 23.1 - - - -
590A ARG 4.4 8.5 - - - +
591A VAL* 3.9 13.2 - - + -
607A VAL* 4.0 8.5 - - + -
633A SER* 3.3 29.4 - - - +
634A THR 3.5 4.7 - - - +
635A VAL* 3.7 31.9 - - + -
643A VAL 4.2 0.2 + - - -
644A LYS* 1.3 72.5 - - - +
646A PHE* 1.3 63.3 + - - +
647A MET* 3.6 9.3 - - + +
656A VAL* 3.3 4.0 - - - -
657A ALA* 2.8 38.1 + - + +
666A TRP* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A SER* 3.0 3.6 - - - -
634A THR* 2.8 59.3 + - + +
636A VAL* 3.8 20.4 - - + -
644A LYS* 3.7 24.0 - - + -
645A LEU* 1.3 74.3 - - - +
647A MET* 1.3 59.2 + - - +
648A ARG 4.3 0.2 + - - -
654A LEU* 4.0 6.7 - - + -
655A GLN 3.6 4.3 - - - -
656A VAL* 3.5 20.2 - - + -
683A MET* 3.9 15.5 - - - +
685A ALA* 4.0 10.8 - - + -
696A ILE* 3.8 28.0 - - + -
698A LEU* 3.3 23.8 - - + -
722A LEU* 3.7 24.7 - - + -
724A TRP* 4.3 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A SER* 3.6 17.3 - - - +
607A VAL* 3.8 23.8 - - - -
630A ASN* 3.6 35.0 - - + -
632A GLU 3.6 4.0 - - - -
633A SER* 3.9 6.1 - - - -
645A LEU* 3.6 10.5 - - + +
646A PHE* 1.3 76.8 - - - +
648A ARG* 1.3 64.0 + - - +
649A GLY 3.5 1.2 + - - -
655A GLN* 3.1 33.2 + - + +
657A ALA* 3.8 22.4 - - + +
670A ILE* 3.8 36.8 - - + -
678A ASP* 4.1 3.3 - - - +
683A MET* 3.9 9.7 - - - +
----------------------------------------------------------
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