Contacts of the strand formed by residues 673 - 683 (chain B) in PDB entry 3LJ1
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 LEU 673 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B LEU* 3.4 30.8 - - + +
671B LYS 4.6 0.2 - - - +
672B ASN* 1.3 81.5 - - + +
674B VAL* 1.3 64.1 + - - +
675B VAL* 4.0 10.3 - - + -
693B SER 3.8 13.9 - - - +
694B PHE* 3.8 13.9 - - + -
699B VAL* 4.3 4.5 - - + -
701B VAL* 4.2 11.0 - - + -
733B CYS* 4.1 13.7 - - - -
735B GLU* 3.1 26.1 + - + +
742B TYR* 4.0 26.5 - - + -
744B ALA* 3.4 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B GLU 6.0 0.4 - - - -
670B LEU 6.0 0.2 - - - +
671B LYS 5.9 1.1 - - - +
672B ASN 4.7 4.7 - - - +
673B LEU* 1.3 78.1 - - - +
675B VAL* 1.3 63.8 + - - +
676B SER* 3.9 0.8 + - - -
692B GLY* 3.1 5.4 - - - -
693B SER* 2.9 50.8 + - - +
695B GLN 6.0 2.0 - - - +
701B VAL* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B GLU* 3.7 36.4 + - + +
670B LEU* 3.7 23.8 - - + +
673B LEU* 4.2 4.9 + - + -
674B VAL* 1.3 78.8 - - - +
676B SER* 1.3 73.7 + - - +
690B PHE* 3.7 28.7 - - + -
691B GLN 4.2 2.5 - - - +
692B GLY* 4.4 1.1 - - - -
701B VAL* 3.8 29.6 - - + -
742B TYR* 3.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 676 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B GLU* 5.1 1.7 - - - +
674B VAL* 3.9 2.5 + - - -
675B VAL* 1.3 78.3 - - - +
677B GLU* 1.3 60.6 + - - +
678B LYS* 3.3 14.3 + - - +
690B PHE* 3.3 21.5 - - - +
691B GLN* 2.6 44.8 + - - +
692B GLY* 4.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 677 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B SER* 1.3 74.9 - - - +
678B LYS* 1.3 63.4 - - - +
679B ILE* 3.4 13.7 + - - +
690B PHE* 3.9 6.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 678 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B DKI 5.6 8.2 - - - -
676B SER* 3.3 11.0 + - - +
677B GLU* 1.3 77.9 - - - +
679B ILE* 1.3 65.7 + - - +
680B LEU* 4.5 15.0 - - + +
690B PHE* 3.2 5.9 - - - +
691B GLN* 3.0 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 679 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A PHE* 4.0 17.7 - - + -
1B DKI 4.4 6.1 + - - -
677B GLU 3.4 13.2 + - - +
678B LYS* 1.3 77.0 - - - +
680B LEU* 1.3 64.7 + - - +
681B GLY 3.7 10.5 - - - +
682B TYR* 3.4 38.6 - - + +
688B VAL* 3.6 24.5 - - + -
689B VAL 3.5 11.7 - - - +
690B PHE* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 680 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B DKI 3.2 80.8 + - + +
678B LYS* 3.8 19.7 + - - +
679B ILE* 1.3 74.5 - - - +
681B GLY* 1.3 55.6 + - - +
689B VAL* 2.7 19.5 + - + +
690B PHE 3.8 9.4 - - - +
691B GLN* 4.0 24.2 - - + +
700B ALA* 3.4 34.1 - - + -
747B LEU* 4.5 8.3 - - + -
751B ASN* 5.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B DKI 3.0 19.3 - - - -
679B ILE* 3.5 7.4 - - - +
680B LEU* 1.3 80.7 - - - +
682B TYR* 1.3 66.7 + - - -
688B VAL* 3.6 1.2 - - - -
689B VAL* 2.7 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A SER* 3.1 44.9 + - - -
686A GLY* 3.2 28.3 - - - +
705A LEU* 4.8 0.2 - - + -
708A PHE* 3.9 6.0 - + - -
1B DKI 3.4 14.9 - - - -
679B ILE* 3.4 42.9 - - + +
681B GLY* 1.3 77.4 - - - -
683B GLY* 1.3 59.9 + - - +
687B THR 3.4 6.3 - - - +
688B VAL* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A GLY* 5.6 3.3 - - - -
1B DKI 4.2 12.8 - - - -
682B TYR* 1.3 77.4 - - - +
684B SER* 1.3 66.1 + - - -
685B SER 3.5 1.4 + - - -
686B GLY* 4.3 1.6 + - - -
687B THR* 2.7 30.9 + - - +
828B ASP* 5.7 2.0 - - - -
----------------------------------------------------------
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