Contacts of the strand formed by residues 564 - 571 (chain A) in PDB entry 3LLT
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 GLY 564 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A HIS* 3.5 8.6 - - - -
560A ASP* 3.9 0.3 - - - -
561A GLY* 2.9 26.5 + - - -
563A PHE* 1.3 80.1 - - - +
565A ARG* 1.3 62.2 + - - -
566A VAL 4.2 0.7 + - - -
581A LYS* 4.0 19.5 - - - -
582A VAL 3.4 8.7 - - - -
583A VAL* 4.1 2.9 - - - -
877A ANP 3.0 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A GLU* 2.8 43.8 + - - -
537A ILE* 5.1 0.6 - - - +
539A HIS* 3.5 24.0 + - + +
540A PHE* 2.8 43.4 + - + +
541A SER* 4.8 1.8 - - - +
542A TRP* 3.5 26.4 - - - +
557A LYS* 3.4 20.3 - - + +
560A ASP* 2.9 32.0 + - - +
564A GLY* 1.3 72.3 - - - -
566A VAL* 1.3 60.2 + - - +
567A LEU* 3.8 14.0 + - + -
580A VAL 3.3 2.8 - - - +
582A VAL* 2.7 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LYS* 3.8 3.5 - - - +
558A MET* 2.8 36.4 + - + -
559A GLY 2.9 18.6 + - - +
565A ARG* 1.3 73.6 - - - +
567A LEU* 1.3 57.1 + - - +
579A ALA* 3.8 30.1 - - + -
580A VAL 3.3 7.2 - - - +
581A LYS* 3.8 28.3 - - + -
630A PHE* 5.8 0.9 - - + -
877A ANP 3.3 51.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A PHE* 4.1 28.9 - - + -
542A TRP* 3.7 46.4 - - + +
548A LEU* 4.8 2.2 - - + -
554A VAL* 4.2 23.1 - - + -
556A ARG 3.4 5.2 - - - +
557A LYS* 3.9 17.5 - - + -
558A MET* 4.1 3.1 - - - -
565A ARG* 4.1 13.9 - - + +
566A VAL* 1.3 73.9 - - - +
568A LEU* 1.3 62.5 + - - +
569A CYS* 3.5 7.4 + - - -
579A ALA* 3.6 0.5 - - - -
580A VAL* 2.8 42.2 + - + +
582A VAL* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A VAL* 3.9 0.3 - - - -
555A ILE* 2.8 47.2 + - + +
556A ARG* 2.8 56.8 + - + +
558A MET* 3.6 24.5 - - + +
567A LEU* 1.3 69.8 - - - +
569A CYS* 1.3 60.5 + - - +
577A TYR* 4.3 20.9 - - + -
578A TYR 3.6 12.6 - - - +
632A PRO* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LEU* 4.3 3.6 - - - -
552A PHE* 3.9 25.1 - - + -
553A LEU 3.1 7.2 - - - +
554A VAL* 3.8 30.1 - - - -
555A ILE* 4.4 4.3 - - - -
567A LEU* 3.9 8.3 - - - -
568A LEU* 1.3 79.8 - - - +
570A GLN* 1.3 60.8 + - - +
576A LYS 4.0 0.2 - - - +
577A TYR* 3.4 5.9 - - - +
578A TYR* 2.8 40.9 + - - +
580A VAL* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A PHE* 4.5 1.3 - - - -
553A LEU* 2.8 53.6 + - + +
555A ILE* 4.1 9.6 - - + +
569A CYS* 1.3 74.3 - - - +
571A HIS* 1.3 66.6 + - - +
572A ILE* 3.6 2.3 + - + +
575A LYS* 2.9 49.1 + - - +
576A LYS 3.6 3.6 - - - +
577A TYR* 3.3 37.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ALA* 3.3 30.0 - - + +
552A PHE* 3.6 31.7 - + - -
569A CYS 4.2 0.8 + - - -
570A GLN* 1.3 74.4 - - - +
572A ILE* 1.3 60.3 + - - +
573A ASP* 3.2 49.7 + - + +
574A ASN* 3.1 27.0 + - - +
575A LYS* 2.9 30.5 + - - +
576A LYS 3.1 7.1 + - - -
578A TYR* 3.7 17.5 - + + -
----------------------------------------------------------
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