Contacts of the strand formed by residues 484 - 492 (chain A) in PDB entry 1NYR
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 GLU 484 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLN* 2.8 36.9 - - - +
377A ARG* 3.1 29.0 + - - -
475A GLN* 3.2 6.7 - - - -
476A VAL* 2.9 38.1 + - + +
478A THR* 4.5 10.1 - - - +
482A LYS* 3.9 10.1 + - + +
483A GLU* 1.3 81.2 - - - +
485A THR* 1.3 63.8 + - - +
486A LEU* 3.6 0.6 + - + -
526A ARG* 4.0 17.9 - - - +
1003A ATP 3.9 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ARG* 3.6 15.9 + - - -
471A LYS* 5.9 0.2 - - - +
473A ASP* 3.2 27.9 + - + +
474A VAL 3.7 0.4 - - - +
475A GLN* 2.7 31.4 + - - +
484A GLU* 1.3 73.5 - - - +
486A LEU* 1.3 62.0 + - - +
487A SER 3.7 12.8 - - - +
488A THR* 4.5 0.7 - - - -
526A ARG* 3.2 24.1 + - - -
1003A ATP 3.2 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A TYR* 2.9 29.6 - - + +
415A PHE* 4.5 1.1 - - + -
474A VAL 2.6 15.3 + - - +
476A VAL* 4.1 21.8 - - + -
484A GLU* 3.6 0.8 + - + -
485A THR* 1.3 73.7 - - - +
487A SER* 1.3 58.1 + - - +
519A GLY 4.3 0.2 - - - +
522A SER* 2.9 38.9 - - - -
526A ARG* 3.7 27.4 - - + -
527A PHE* 4.3 18.8 - - + -
530A PHE* 3.9 39.3 - - + -
1003A ATP 3.0 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ILE* 3.6 25.4 - - - -
410A TYR* 2.6 29.1 + - - -
474A VAL* 2.9 35.3 + - - +
485A THR* 3.7 2.7 - - - +
486A LEU* 1.3 75.7 - - - +
488A THR* 1.3 62.9 + - - +
519A GLY 3.0 16.6 - - - -
520A VAL 2.7 17.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ILE* 4.4 4.4 - - - +
471A LYS* 3.6 2.4 - - - +
472A LEU 3.5 6.1 + - - -
473A ASP* 2.9 23.6 + - - -
485A THR* 4.5 0.7 - - - -
487A SER* 1.3 75.6 - - - +
489A ALA* 1.3 54.2 + - - +
490A GLN* 3.1 31.1 + - - +
517A HIS 4.4 0.2 - - - -
518A ARG* 2.8 13.9 - - - +
519A GLY* 2.8 43.0 + - - +
1003A ATP 3.8 36.6 - - - +
1004A THR* 4.4 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A PHE* 3.4 33.4 - - + -
402A VAL* 4.2 24.9 - - + -
403A VAL* 4.9 4.7 - - + -
406A ILE* 5.1 4.9 - - + +
471A LYS* 3.5 0.5 - - - -
472A LEU* 2.9 35.3 + - + -
488A THR* 1.3 73.4 + - - +
490A GLN* 1.3 61.4 + - - +
516A ILE* 4.8 0.9 - - + -
517A HIS 3.3 4.3 - - - -
518A ARG* 3.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A PHE* 4.1 1.1 - - - -
466A ALA* 4.7 0.6 - - - +
468A TYR* 2.6 39.3 + - + -
470A PRO 3.6 13.5 - - - +
471A LYS* 3.2 16.6 - - + +
488A THR* 3.1 19.5 + - - +
489A ALA* 1.3 79.3 - - - +
491A LEU* 1.3 61.8 + - - +
515A VAL 3.4 1.2 - - - +
516A ILE* 3.0 11.6 - - - +
517A HIS* 2.6 61.8 + - + +
1003A ATP 3.1 24.4 + - - -
1004A THR* 3.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 3.1 35.2 - - + -
399A PHE* 4.2 15.8 - - + -
443A ALA* 4.1 7.6 - - + +
446A MET* 4.5 7.4 - - + -
447A LEU* 3.9 46.4 - - + +
450A ALA* 6.1 0.4 - - + -
468A TYR* 4.0 0.9 - - - +
469A GLY* 3.5 24.6 - - - -
470A PRO* 3.4 18.2 + - + +
489A ALA 4.4 0.6 + - - -
490A GLN* 1.3 71.5 - - - +
492A ASP* 1.3 58.2 + - - +
493A PHE* 4.2 24.9 + - + -
514A VAL* 4.4 8.1 - - + -
515A VAL 3.8 0.9 - - - -
516A ILE* 4.6 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A MET* 5.5 0.2 - - - +
468A TYR* 3.1 27.8 - - + +
491A LEU* 1.3 74.2 - - - +
493A PHE* 1.3 61.7 + - - +
494A LEU* 3.0 15.4 + - - +
495A LEU* 3.1 32.9 - - - +
496A PRO* 4.1 4.8 - - - +
514A VAL* 3.5 3.9 - - - +
515A VAL* 2.7 46.8 + - + +
517A HIS* 3.1 31.7 + - + +
----------------------------------------------------------
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