Contacts of the strand formed by residues 513 - 519 (chain N) in PDB entry 4WQS
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 ILE 513 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N PRO* 4.8 9.9 - - + +
98N PRO* 4.5 2.2 - - + -
99N ALA 3.6 8.5 - - - +
100N ALA* 4.5 7.9 - - + +
128N TYR* 4.9 0.2 - - - +
458N ALA 4.0 6.5 - - - +
461N ILE* 4.3 11.2 - - + -
462N GLN* 3.1 68.2 - - + +
465N LEU* 4.2 8.7 - - + +
466N LYS* 6.3 0.4 - - - -
510N GLU 3.3 20.4 + - - +
511N TRP* 2.4 22.5 + - + +
512N MET* 1.3 77.3 - - + +
514N LEU* 1.3 64.3 + - - +
515N GLU* 4.2 15.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 514 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096M ALA* 4.4 21.1 - - + -
15N PRO* 6.2 0.4 - - - -
18N ILE* 6.1 3.1 - - + -
95N LEU* 3.1 15.3 - - + +
98N PRO* 2.8 4.8 - - - +
99N ALA* 2.5 42.5 + - + +
100N ALA* 3.8 6.7 - - - +
101N HIS* 3.7 37.2 - - + +
511N TRP 4.6 4.3 - - - +
512N MET 4.1 3.8 - - - +
513N ILE* 1.3 81.8 - - - +
515N GLU* 1.3 61.1 + - - +
516N ALA 4.3 14.8 - - - +
517N VAL* 5.4 3.1 - - + -
518N PRO* 5.7 2.9 - - + -
578N VAL* 4.8 10.3 - - + -
582N LEU* 5.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 515 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N PRO* 3.9 23.2 - - + +
19N ARG* 4.3 11.8 + - - +
94N GLU* 2.8 34.1 - - - +
95N LEU* 2.8 28.6 + - + +
98N PRO* 3.6 20.1 - - + +
462N GLN* 3.6 17.6 + - - +
466N LYS* 6.2 0.3 - - - -
513N ILE* 4.2 8.1 - - + +
514N LEU* 1.3 74.8 - - - +
516N ALA* 1.3 61.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 516 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N PRO* 4.4 3.8 - - + +
18N ILE* 4.0 20.1 - - + +
19N ARG* 2.8 44.6 - - - +
92N HIS* 5.6 0.9 - - + -
93N ILE 3.5 7.2 - - - -
94N GLU* 4.4 0.4 - - - +
95N LEU* 3.5 0.6 - - - +
514N LEU* 3.5 14.8 - - - +
515N GLU* 1.3 80.6 - - + +
517N VAL* 1.3 61.3 + - - +
518N PRO* 3.4 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 517 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N ILE* 4.4 0.6 - - - +
92N HIS* 3.1 4.5 - - - -
93N ILE* 2.8 52.3 + - + +
95N LEU* 3.5 39.5 - - + -
514N LEU* 5.4 3.8 - - + -
516N ALA* 1.3 71.7 - - - +
518N PRO* 1.3 77.1 - - + +
519N VAL* 3.7 3.5 - - - +
544N TYR* 5.7 2.5 - - + -
547N LEU* 4.9 18.4 - - + -
581N LEU* 5.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 518 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093M GLN 4.5 0.7 - - - +
1094M ALA 3.7 25.5 - - - +
1096M ALA* 4.9 9.4 - - - +
18N ILE* 3.3 27.8 - - + -
21N TRP* 3.5 28.5 - - + -
90N MET* 3.9 8.7 - - - -
91N GLY 3.2 8.3 - - - +
514N LEU* 5.7 3.8 - - + -
516N ALA 3.4 9.6 - - - +
517N VAL* 1.3 97.3 - - + +
519N VAL* 1.3 60.7 + - - +
520N LEU 4.4 0.5 + - - -
544N TYR* 4.4 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 519 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094M ALA* 4.9 0.2 - - - -
26N VAL* 4.0 8.1 - - + -
44N LEU* 4.6 9.4 - - + -
50N PHE* 4.1 10.7 - - + -
90N MET* 2.9 31.6 - - - +
91N GLY* 2.7 36.7 + - - +
92N HIS 3.8 1.6 - - - +
93N ILE* 3.7 21.3 - - + -
517N VAL 3.7 8.1 - - - +
518N PRO* 1.3 78.1 - - - +
520N LEU* 1.3 66.7 + - - +
525N ARG* 3.7 23.1 - - - +
544N TYR* 4.1 14.8 - - + -
----------------------------------------------------------
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