Contacts of the strand formed by residues 662 - 669 (chain A) in PDB entry 3S3J
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 HIS 662 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ALA 4.5 8.0 + - - +
628A GLY* 3.3 35.0 + - - -
629A LEU* 3.4 29.1 - - + +
656A PRO* 5.0 1.3 - - + -
658A HIS* 3.1 41.4 + - + +
659A MET 5.0 2.0 - - - -
660A GLY 4.1 9.0 - - - -
661A LEU* 1.3 95.3 + - - +
663A LYS* 1.3 59.8 + - - +
680A ARG 3.6 1.7 - - - +
682A VAL* 2.9 38.3 + - - +
684A ILE* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A GLY* 3.7 18.7 - - - -
627A ALA 5.1 2.8 + - - +
629A LEU* 4.1 4.1 - - - +
661A LEU* 4.9 7.9 - - + +
662A HIS* 1.3 72.0 - - - +
664A LEU* 1.3 63.2 + - - +
665A VAL* 3.9 11.5 + - + +
679A PHE* 3.9 38.1 - - + -
680A ARG 3.4 7.0 - - - +
681A ASN* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ILE* 4.4 14.6 - - + -
593A ILE* 6.0 2.7 - - + -
605A ALA* 3.6 30.7 - - + -
624A VAL* 3.6 26.7 - - + -
625A GLU 3.5 19.3 - - - +
626A GLY 4.4 0.2 - - - +
629A LEU* 3.9 22.1 - - + +
630A THR* 4.3 11.9 - - + -
654A LEU* 3.8 15.0 - - + -
663A LYS* 1.3 73.9 - - - +
665A VAL* 1.3 60.8 + - - +
666A VAL* 4.9 5.2 - - + -
679A PHE* 3.1 9.6 - - - +
680A ARG* 3.0 40.1 + - + +
682A VAL* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A THR 3.9 0.2 - - - +
624A VAL* 3.4 4.3 - - - +
625A GLU* 2.9 47.2 + - + +
626A GLY* 5.2 1.8 - - - -
663A LYS* 4.0 18.8 - - + +
664A LEU* 1.3 79.6 - - - +
666A VAL* 1.3 70.4 + - - +
677A LYS* 6.1 4.5 - - + -
678A GLY 3.6 9.0 - - - +
679A PHE* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A ILE* 4.3 7.4 - - + -
591A ILE* 3.4 32.5 - - + -
607A VAL* 4.0 22.0 - - + -
622A PHE* 4.0 8.1 - - + -
623A THR 3.2 9.9 - - - +
624A VAL* 3.9 22.4 - - + -
664A LEU* 4.9 4.5 - - + -
665A VAL* 1.3 87.0 - - - +
667A ASN* 1.3 71.6 + - - +
677A LYS* 3.3 10.4 - - - +
678A GLY 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A THR 3.9 0.6 + - - +
622A PHE* 3.2 3.8 - - - -
623A THR* 2.7 56.5 + - + +
666A VAL* 1.3 78.8 - - - +
668A PHE* 1.3 62.1 + - - +
669A GLU* 2.6 30.9 + - - +
675A ALA* 3.6 11.5 - - - +
676A VAL 3.4 2.9 - - - +
677A LYS* 3.1 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A ILE* 3.8 20.9 - - + -
609A LEU* 4.1 22.7 - - + -
617A LEU* 4.1 15.3 - - + -
620A CYS* 3.8 31.6 - - + -
621A THR 3.5 4.9 - - - -
622A PHE* 3.4 41.7 - + + -
648A VAL* 4.7 4.5 - - + -
667A ASN* 1.3 73.9 - - - +
669A GLU* 1.3 79.1 + - - +
670A SER* 3.7 15.3 - - - -
673A LEU* 3.9 11.4 - - + -
674A LYS 4.1 0.3 - - - -
675A ALA 3.5 5.4 + - - -
676A VAL* 2.7 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A GLY 4.2 1.3 - - - +
620A CYS* 3.3 2.4 - - - -
621A THR* 2.8 46.3 + - + +
667A ASN* 2.6 33.1 + - - +
668A PHE* 1.3 78.6 - - - +
670A SER* 1.3 66.6 + - - +
673A LEU 3.7 2.5 - - - -
674A LYS* 3.3 26.5 + - - +
675A ALA* 2.9 29.9 + - - +
----------------------------------------------------------
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