Contacts of the strand formed by residues 613 - 618 (chain D) in PDB entry 3A98
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 ILE 613 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D LEU* 5.0 5.4 - - + -
608D LEU* 3.6 27.1 - - + -
609D PRO 3.5 15.7 - - - +
610D VAL* 2.8 25.4 + - + +
611D ALA 3.4 2.5 - - - +
612D ASP* 1.3 76.4 - - - +
614D LYS* 1.3 66.1 + - - +
615D ALA 4.0 9.9 - - - +
616D VAL* 4.7 2.0 - - + -
644D ILE* 3.2 38.1 - - + -
645D LEU 3.4 7.2 - - - +
646D TYR* 3.9 5.6 - - + -
673D LEU* 3.7 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 614 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D ASP 4.8 4.0 - - - +
613D ILE* 1.3 75.8 - - - +
615D ALA* 1.3 65.7 + - + +
645D LEU* 2.5 20.7 + - + +
646D TYR* 3.5 18.2 - - - +
647D ASP* 3.3 34.4 - - - +
673D LEU* 4.8 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 615 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D ILE* 3.6 2.3 - - - -
614D LYS* 1.3 85.7 - - + +
616D VAL* 1.3 67.3 + - - +
617D VAL* 5.0 2.0 - - + -
645D LEU* 2.9 38.1 + - + +
673D LEU* 4.2 9.2 - - - -
675D LYS* 6.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 616 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D ILE* 4.7 3.6 - - + -
615D ALA* 1.3 77.3 - - - +
617D VAL* 1.3 73.3 + - - +
618D THR* 4.4 1.4 + - - +
642D PHE* 4.6 8.7 - - + -
643D SER 3.3 15.9 - - - +
644D ILE* 4.5 9.2 - - + -
666D THR* 5.9 4.3 - - - -
669D LEU* 3.7 39.9 - - + -
670D ASN* 4.6 13.2 - - - +
673D LEU* 3.7 22.4 - - + +
675D LYS* 5.9 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 617 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D ALA* 4.5 2.9 - - + +
616D VAL* 1.3 78.3 - - - +
618D THR* 1.3 60.7 + - - +
621D ASP* 3.8 23.6 - - + +
622D CYS* 3.6 4.7 - - - -
623D PRO* 3.6 15.7 - - + -
642D PHE* 3.0 7.4 - - - +
643D SER* 2.6 66.4 + - - +
645D LEU* 3.4 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 618 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D VAL* 5.6 1.1 - - - +
617D VAL* 1.3 76.2 - - - +
619D GLY* 1.3 77.0 + - - +
620D LYS 3.5 0.2 + - - -
621D ASP* 3.0 26.9 + - - +
622D CYS* 3.4 6.3 - - - -
638D LEU 5.0 0.7 + - - -
641D ALA 3.7 5.6 + - - -
642D PHE* 4.7 4.3 - - - -
662D TYR* 2.6 31.0 + - - +
666D THR* 5.9 0.9 - - - -
----------------------------------------------------------
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