Contacts of the strand formed by residues 441 - 447 (chain A) in PDB entry 3N9V
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 441 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A THR* 4.3 15.9 - - + -
393A SER 3.1 9.0 + - - +
394A ILE* 3.3 22.3 - - + -
395A CYS 2.9 25.5 + - - -
439A HIS* 3.1 1.8 - - - +
440A ASP* 1.3 85.2 - - + +
442A ILE* 1.3 71.5 + - - +
443A LEU* 4.5 4.7 - - + -
529A LYS 3.7 2.9 - - - -
531A LYS 4.5 5.8 - - - +
533A ILE* 4.0 24.0 - - + -
558A ILE* 4.2 34.8 - - + -
559A GLY 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A CYS* 3.2 10.5 - - + +
397A VAL* 4.7 3.6 - - + -
436A ILE* 3.3 44.6 - - + +
437A SER* 3.8 19.3 - - - +
439A HIS* 4.3 11.2 - - + +
441A VAL* 1.3 77.8 - - - +
443A LEU* 1.3 73.4 + - - +
444A TRP* 5.0 1.1 - - + -
491A PHE* 3.9 25.8 - - + -
528A TRP* 3.3 7.1 - - - +
529A LYS* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 4.3 25.4 - - + -
269A ALA* 4.7 12.6 - - + -
298A CYS* 4.4 16.4 - - + -
394A ILE* 5.3 0.9 - - + -
395A CYS 2.9 7.4 + - - +
396A VAL* 3.1 19.4 - - + +
397A VAL* 2.8 26.2 + - - +
441A VAL* 4.5 14.4 - - + -
442A ILE* 1.3 82.5 - - - +
444A TRP* 1.3 60.2 + - - +
445A LEU* 4.2 2.2 - - + -
526A ILE* 5.6 1.6 - - + -
527A LEU 3.7 3.4 - - - +
528A TRP* 3.7 19.1 - - + -
533A ILE* 4.8 2.2 - - + -
556A PHE* 4.1 28.5 - - + -
558A ILE* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 3.4 28.9 - - + +
399A SER* 2.8 30.2 + - - -
401A LEU* 5.5 1.6 - - + -
415A TYR* 3.4 37.9 - + - -
418A ILE* 3.6 30.5 - - + -
419A CYS* 3.9 14.8 - - - -
436A ILE* 4.1 18.4 - - + -
442A ILE* 4.2 1.0 + - + -
443A LEU* 1.3 73.0 - - - +
445A LEU* 1.3 73.3 + - - +
448A LEU* 3.8 5.5 - - + +
488A PHE* 3.5 33.5 - + + -
491A PHE* 4.2 20.6 - + + -
525A ARG 4.2 0.2 - - - +
526A ILE* 3.4 2.4 - - - +
527A LEU* 2.7 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA* 4.1 21.8 - - + -
270A GLY 3.8 24.0 - - - +
271A THR* 4.2 7.2 - - - -
298A CYS 4.3 7.0 - - - +
300A GLY* 4.0 6.7 - - - -
349A LEU* 4.4 3.6 - - + -
396A VAL* 4.2 21.8 - - + -
397A VAL 2.8 12.1 + - - +
398A ASN* 3.2 34.6 - - + +
399A SER* 3.1 20.8 + - - -
443A LEU* 5.4 2.5 - - + +
444A TRP* 1.3 84.6 - - - +
446A GLY* 1.3 60.8 + - - +
448A LEU* 4.7 1.3 - - - -
525A ARG 3.3 11.0 - - - +
526A ILE* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 3.2 20.0 + - - -
302A GLN* 3.5 6.7 - - - -
398A ASN* 3.8 0.4 - - - -
399A SER 3.3 11.4 - - - -
445A LEU* 1.3 77.3 - - - +
447A ASP* 1.3 61.4 + - - -
448A LEU* 3.4 8.5 + - - +
524A ASP* 3.4 2.1 - - - -
525A ARG 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASN* 2.9 25.1 + - - +
302A GLN* 3.6 17.5 - - + +
399A SER 3.3 5.3 + - - +
400A HIS* 3.3 27.3 + - + -
401A LEU 3.2 21.1 + - - -
446A GLY* 1.3 68.1 - - - -
448A LEU* 1.3 57.6 + - - +
449A ASN* 3.1 30.9 + - - +
523A CYS* 3.5 7.0 - - - +
524A ASP* 3.4 22.0 - - - +
549A HIS* 3.3 10.4 + - - -
----------------------------------------------------------
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