Contacts of the strand formed by residues 501 - 510 (chain A) in PDB entry 1NQG
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 GLN 501 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TYR* 2.4 39.5 + - + +
482A ASP 3.3 4.5 - - - +
483A TYR* 4.6 8.5 - - + -
499A ALA* 3.2 3.0 - - - +
500A LYS* 1.3 101.9 - - + +
502A GLN* 1.3 63.0 + - - +
503A VAL* 5.8 0.7 - - + -
522A TYR* 4.1 11.6 - - + +
524A GLY* 3.0 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY 5.5 0.8 - - - -
52A VAL 3.0 26.1 + - - +
53A ASP* 3.9 21.4 + - - +
481A TYR* 3.3 5.1 - - - -
482A ASP* 3.2 39.8 + - + +
484A VAL* 6.1 0.2 - - - +
499A ALA* 4.6 7.3 + - + +
501A GLN* 1.3 77.3 - - - +
503A VAL* 1.3 71.0 + - - +
504A LYS* 3.5 22.2 - - + +
521A GLN* 3.4 12.5 + - - -
522A TYR* 3.4 5.8 - - - +
523A LEU* 2.6 39.7 - - + +
524A GLY 4.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A VAL* 5.3 6.5 - - + -
480A SER 3.7 7.0 - - - +
481A TYR* 3.7 21.5 - - + -
501A GLN* 5.4 1.1 - - + -
502A GLN* 1.3 82.2 - - - +
504A LYS* 1.3 67.6 + - - +
505A TYR* 5.6 1.6 - - + -
520A TYR* 3.6 20.2 - - + +
521A GLN* 3.2 5.5 - - - -
522A TYR* 2.7 54.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG 3.3 17.0 + - - +
48A ARG* 3.6 17.3 - - - +
49A LEU 2.5 27.4 + - - +
50A PRO* 4.3 1.0 - - - +
51A GLY 4.1 4.4 - - - +
52A VAL 3.3 22.0 + - - +
478A THR 4.5 1.6 - - - -
479A VAL* 3.3 6.6 - - - +
480A SER* 2.9 47.8 + - - +
482A ASP* 4.4 4.0 + - - -
502A GLN* 3.5 32.5 - - + +
503A VAL* 1.3 83.0 - - - +
505A TYR* 1.3 60.8 + - - +
520A TYR 3.4 5.8 - - - +
521A GLN* 3.3 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PHE* 4.1 9.4 - + - -
477A HIS* 2.9 42.6 + - + +
478A THR 3.6 6.1 - - - -
479A VAL* 3.3 29.8 - - + -
503A VAL* 5.6 2.5 - - + -
504A LYS* 1.3 73.7 - - - +
506A GLN* 1.3 78.7 + - - +
507A LEU* 4.0 9.9 - - + -
518A ILE 4.0 0.7 - - - +
519A THR* 3.4 2.4 - - - -
520A TYR* 2.9 53.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 4.4 0.5 + - - -
37A TRP* 3.6 30.8 + - + +
48A ARG* 3.7 6.7 - - - +
476A THR 4.5 0.2 - - - -
477A HIS* 3.6 2.9 - - - -
478A THR* 3.0 44.9 + - + +
505A TYR* 1.3 82.3 - - - +
507A LEU* 1.3 60.3 + - - +
508A ASP* 3.5 30.1 - - - +
517A GLY* 4.3 9.5 - - - -
518A ILE 3.7 6.3 - - - +
519A THR* 2.5 47.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A LEU* 4.9 12.3 - - + -
476A THR 3.5 4.9 - - - +
477A HIS* 2.9 48.2 - - + +
505A TYR* 4.0 10.8 - - + -
506A GLN* 1.3 74.8 - - - +
508A ASP* 1.3 62.0 + - - +
509A TRP* 3.7 28.3 - - + -
516A TRP 3.9 0.2 - - - +
517A GLY* 3.2 4.9 - - - -
518A ILE* 2.9 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 2.3 44.1 + - - +
474A PRO 3.9 0.2 - - - +
475A LEU* 3.7 1.2 - - - +
476A THR* 2.8 51.0 + - - +
478A THR* 4.7 7.1 + - - -
506A GLN* 3.5 26.3 - - - +
507A LEU* 1.3 75.9 + - - +
509A TRP* 1.4 65.2 + - - +
510A GLN* 5.4 1.3 - - - +
516A TRP 3.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO* 3.2 21.1 - - + +
475A LEU* 3.3 21.5 - - + -
507A LEU* 3.7 36.6 - - + -
508A ASP* 1.4 82.3 - - - +
510A GLN* 1.3 86.9 + - - +
511A LEU* 4.6 7.1 - - + +
516A TRP* 2.8 73.9 + + + +
518A ILE* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 5.2 0.2 - - - +
474A PRO* 4.3 14.8 + - - +
508A ASP* 5.4 0.8 - - - +
509A TRP* 1.3 103.1 + - - +
511A LEU* 1.3 68.9 + - - +
512A TYR 5.8 0.7 - - - +
513A ASP* 5.8 2.0 - - - +
514A PHE 3.2 10.8 - - - +
515A ASP* 3.3 29.0 + - + +
----------------------------------------------------------
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