Contacts of the strand formed by residues 556 - 560 (chain A) in PDB entry 3I7N
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 CYS 556 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A VAL* 5.8 3.1 - - - -
541A LEU* 4.6 12.3 - - - -
542A ASP 3.3 22.7 - - - -
543A ILE* 3.8 14.8 - - + -
554A PRO 5.1 0.7 - - - +
555A LEU* 1.3 75.9 - - - +
557A ALA* 1.3 78.8 + - - +
568A ILE* 3.3 7.3 - - - +
569A LEU* 2.5 50.9 + - + +
570A LYS 3.7 17.9 - - - +
571A LEU* 6.2 1.8 - - + -
574A PHE* 6.5 0.4 - - + -
593A MET* 4.3 4.7 - - - -
616A LEU* 5.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 3.9 2.3 - - - +
542A ASP* 3.8 20.0 + - + +
556A CYS* 1.3 90.5 - - - +
558A ILE* 1.3 64.1 + - - +
567A ARG 3.2 14.4 - - - +
568A ILE* 4.7 5.8 - - + -
569A LEU* 5.1 0.4 - - - -
591A ILE* 4.3 9.1 - - + +
592A LEU 6.4 0.2 - - - -
593A MET* 4.8 7.5 - - + +
602A LEU* 3.9 27.8 - - + -
616A LEU* 5.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 4.1 17.0 - - + -
534A MET* 4.3 6.1 - - + -
538A VAL* 3.5 30.5 - - + -
540A CYS 3.4 15.9 - - - +
541A LEU* 3.7 14.6 - - + -
556A CYS* 5.8 0.2 - - - -
557A ALA* 1.3 78.2 - - - +
559A GLY* 1.3 64.4 + - - +
560A LEU* 3.6 22.4 - - + -
565A SER 3.6 0.3 - - - +
566A ALA* 3.0 24.0 - - - +
567A ARG* 3.1 31.0 + - + +
569A LEU* 3.9 16.4 - - + -
591A ILE* 4.3 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ALA* 2.6 36.2 + - - +
540A CYS* 3.2 18.6 + - - -
558A ILE* 1.3 76.6 - - - +
560A LEU* 1.3 59.3 + - - +
565A SER 2.9 11.4 - - - -
566A ALA* 4.3 2.5 - - - -
588A PRO* 3.9 13.0 - - - -
591A ILE* 4.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A MET* 3.9 24.0 - - + -
535A GLU* 4.5 1.6 - - + -
536A HIS* 3.6 41.7 - - + +
537A GLU 3.2 6.7 - - - +
538A VAL* 3.8 14.4 - - + +
539A ALA* 3.9 5.6 - - - -
558A ILE* 3.6 35.0 - - + -
559A GLY* 1.3 75.2 - - - +
561A TRP* 1.3 59.1 + - - +
563A ASP* 3.5 23.0 - - - +
564A ILE* 3.7 2.6 - - - -
565A SER* 3.1 13.8 + - - +
567A ARG* 4.3 14.4 - - - +
588A PRO* 3.4 19.8 - - - +
----------------------------------------------------------
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