Contacts of the strand formed by residues 582 - 587 (chain A) in PDB entry 3K72
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 ASP 582 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.5 6.5 + - - -
509A LEU* 3.8 5.2 - - - +
571A GLY* 3.5 0.3 - - - -
572A GLY 3.1 23.9 + - - -
573A GLN 3.1 14.5 + - - +
574A ASP* 4.2 1.0 - - - +
575A LEU* 3.2 21.0 + - + +
576A THR* 3.2 43.0 + - - +
578A ASP* 4.1 3.3 - - - +
580A LEU 3.7 7.0 - - - +
581A VAL* 1.3 84.4 - - - +
583A LEU* 1.3 63.4 + - - +
593A LEU* 4.8 3.1 - - + -
594A LEU 4.1 5.4 - - - +
595A ARG* 3.5 24.1 - - - +
596A THR* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.7 16.4 - - + -
24A GLN* 4.2 0.2 - - - -
507A THR* 4.1 13.0 - - + -
509A LEU* 4.4 10.8 - - + -
521A VAL* 3.7 38.8 - - + -
534A VAL* 5.2 1.8 - - + -
569A LEU* 4.7 1.3 - - + -
570A SER 4.1 3.4 - - - +
571A GLY* 3.9 22.0 - - - +
582A ASP* 1.3 76.4 - - - +
584A ALA* 1.3 70.6 + - - +
585A VAL* 3.9 19.5 + - + -
592A LEU 4.0 0.2 - - - +
593A LEU* 3.0 17.6 - - - +
594A LEU* 3.1 42.9 + - + +
596A THR* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.1 12.1 - - + +
23A VAL 5.8 0.2 - - - -
24A GLN* 3.9 5.8 - - + +
30A VAL* 4.2 20.2 - - + -
569A LEU* 3.2 5.9 - - - +
570A SER 3.1 38.8 + - - +
583A LEU* 1.3 75.5 - - - +
585A VAL* 1.3 61.8 + - - +
586A GLY 4.1 0.4 - - - -
591A VAL* 5.0 2.7 - - + -
592A LEU 3.6 6.1 - - - +
593A LEU* 3.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 4.2 11.2 - - + -
565A PHE* 3.6 26.1 - - + -
566A GLY* 3.4 33.2 - - - +
568A ALA 3.8 4.7 - - - +
569A LEU* 3.8 17.3 - - + -
583A LEU* 3.9 24.0 - - + -
584A ALA* 1.3 76.4 - - - +
586A GLY* 1.3 62.3 + - - +
587A ALA* 3.9 0.9 + - - +
591A VAL* 3.7 3.3 - - - +
592A LEU* 3.1 35.2 + - + +
594A LEU* 5.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 3.7 13.0 - - - -
20A ASP 5.8 1.1 - - - -
22A VAL* 3.7 14.5 - - - +
566A GLY 3.0 23.6 + - - -
567A GLN* 3.7 9.5 + - - +
568A ALA* 3.1 16.5 + - - +
585A VAL* 1.3 71.7 - - - +
587A ALA* 1.3 59.7 + - - -
591A VAL* 3.7 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 2.6 23.5 + - - +
562A LEU* 3.4 20.6 - - + -
564A TYR 4.0 1.3 - - - -
565A PHE* 3.4 29.2 - - + -
567A GLN* 3.6 6.1 - - - +
585A VAL 4.8 1.3 - - - +
586A GLY* 1.3 74.1 - - - -
588A ARG* 1.3 64.3 + - - +
589A GLY 2.9 3.3 + - - -
590A GLN* 2.7 26.4 + - + +
591A VAL* 5.2 0.2 - - - -
592A LEU* 5.3 2.5 - - + -
----------------------------------------------------------
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