Contacts of the strand formed by residues 560 - 566 (chain A) in PDB entry 4NPJ
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 PRO 560 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LEU* 3.9 15.3 - - + -
558A PRO* 3.4 9.0 - - + +
559A ASN* 1.3 82.4 - - - +
561A VAL* 1.3 59.8 + - - +
575A ILE* 3.8 0.3 - - - -
576A ARG* 3.0 40.9 + - + +
579A THR* 3.1 32.1 - - + +
582A PRO* 3.7 31.2 - - + -
584A TRP* 3.9 11.3 + - + -
604A VAL* 4.3 2.5 - - + -
605A ARG 3.3 7.9 - - - +
613A LEU* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ASN 4.5 0.7 - - - +
560A PRO* 1.3 75.2 - - - +
562A VAL* 1.3 70.2 + - - +
563A GLN* 6.4 0.4 - - + -
572A GLU* 4.5 17.5 - - + +
573A SER* 3.5 27.1 - - - +
574A LYS 3.6 10.1 - - - +
575A ILE* 4.1 16.4 - - + -
584A TRP* 4.4 1.1 - - - -
603A GLU 3.7 0.9 - - - +
604A VAL* 3.4 2.5 - - - -
605A ARG* 2.8 57.6 + - + +
607A GLU* 4.5 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 3.8 18.6 - - + -
561A VAL* 1.3 74.2 - - - +
563A GLN* 1.3 62.5 + - - +
564A MET* 4.0 20.3 + - + +
572A GLU* 3.4 8.2 - - - +
573A SER* 2.9 39.5 + - - +
584A TRP* 3.3 39.9 - - + -
602A VAL* 3.7 29.2 - - + -
603A GLU 3.4 4.3 - - - +
604A VAL* 4.4 5.8 - - + -
646A ILE* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A VAL* 4.2 0.8 + - + -
562A VAL* 1.3 73.9 - - - +
564A MET* 1.3 66.7 + - - +
565A SER* 5.0 5.8 + - - +
570A ALA* 4.9 14.1 - - + +
571A GLN 3.6 9.9 - - - +
572A GLU* 3.1 26.6 - - + +
601A GLU 3.6 1.9 - - - +
602A VAL* 3.6 1.6 - - - -
603A GLU* 2.9 45.5 + - + +
605A ARG* 3.7 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU* 3.6 32.1 - - + -
542A LEU* 4.5 7.2 - - + -
562A VAL* 4.0 27.1 - - + +
563A GLN* 1.3 75.5 - - - +
565A SER* 1.3 61.2 + - - +
570A ALA* 3.3 3.6 - - - +
571A GLN 2.8 40.6 + - - +
573A SER 4.4 1.8 - - - +
588A PHE* 3.5 41.3 - - + -
590A PHE* 3.7 15.7 - - + -
600A LEU* 4.2 9.0 - - + -
601A GLU 3.3 4.0 - - - +
602A VAL* 4.0 22.4 - - + -
648A MET* 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A GLN* 5.0 6.2 + - - +
564A MET* 1.3 78.0 - - - +
566A VAL* 1.3 63.1 + - - +
567A GLY 4.0 11.7 - - - -
569A LYS 3.1 16.6 - - - -
570A ALA* 4.2 9.0 - - - -
590A PHE* 4.5 1.8 - - - -
599A ASP 3.6 0.9 - - - +
600A LEU* 3.6 4.8 - - - +
601A GLU* 2.8 48.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
538A LEU* 3.9 19.7 - - + -
565A SER* 1.3 76.8 - - - +
567A GLY* 1.3 60.9 + - - +
568A HIS* 3.0 9.5 + - - -
569A LYS* 3.2 21.3 + - + +
590A PHE* 4.4 15.5 - - + -
591A PHE 5.1 3.8 - - - +
592A ILE* 3.8 33.0 - - + -
598A GLN* 3.7 34.4 + - + +
599A ASP 3.7 15.3 - - - +
600A LEU* 4.2 8.5 - - + +
620A LEU* 4.4 3.6 - - + -
----------------------------------------------------------
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