Contacts of the strand formed by residues 414 - 419 (chain A) in PDB entry 1N1M
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 TYR 414 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA 4.1 0.4 - - - +
410A LEU* 3.5 2.9 - - - +
411A THR* 2.8 42.1 + - - +
413A ASP* 1.3 104.1 - - + +
415A LEU* 1.3 60.7 - - - +
416A TYR* 4.0 26.4 - - + -
433A LYS* 3.7 42.8 + - + -
434A ILE 3.5 19.5 - - - +
435A GLN* 3.7 33.3 + - + -
436A LEU* 3.2 12.3 - - - -
441A LYS 5.0 2.5 - - - -
443A THR* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 4.2 19.1 - - + -
384A ILE* 3.6 30.5 - - + -
397A ILE* 4.5 9.0 - - + -
407A ILE* 3.5 24.9 - - + -
409A ALA 3.5 3.8 - - - +
410A LEU* 3.6 24.0 - - + -
414A TYR* 1.3 76.1 - - - +
416A TYR* 1.3 77.0 + - - +
417A TYR* 3.8 4.8 + - + -
433A LYS* 3.3 2.1 - - - -
434A ILE* 3.0 39.3 + - + +
436A LEU* 3.2 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 3.6 0.3 - - - +
408A GLU* 2.8 22.6 + - - -
409A ALA* 2.6 39.0 + - + +
411A THR* 4.3 16.6 + - + -
414A TYR* 4.0 23.7 - - + -
415A LEU* 1.3 80.0 - - - +
417A TYR* 1.3 63.9 + - - +
431A LEU* 4.4 2.0 - - + -
432A TYR 3.4 4.9 - - - +
433A LYS* 3.6 36.1 + - + +
445A LEU* 3.7 19.5 - - + -
461A PHE* 3.4 40.4 - + + -
465A ALA* 4.7 4.3 - - + -
468A TYR* 5.2 0.9 - + - -
485A SER* 3.6 28.0 + - - -
488A ASP* 5.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ILE* 3.7 19.7 - - + -
398A THR* 4.0 21.3 - - + +
402A TRP* 4.0 14.1 - + - -
404A VAL* 3.8 14.6 - - + -
406A GLY 3.3 14.1 - - - +
407A ILE* 4.0 1.3 - - - -
408A GLU* 4.0 3.4 - - - +
415A LEU* 3.8 18.2 - - + -
416A TYR* 1.3 75.8 - - - +
418A ILE* 1.3 74.9 + - - +
419A SER* 3.7 20.0 - - - -
421A GLU* 4.5 1.2 + - - -
431A LEU* 3.3 5.9 - - - +
432A TYR* 2.6 77.5 + + + +
433A LYS 4.8 0.2 - - - -
434A ILE* 4.1 17.5 - - + -
442A VAL* 3.9 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 3.4 3.8 - - - +
405A ILE* 2.5 54.4 + - + +
406A GLY 2.9 13.2 + - - +
408A GLU* 3.9 24.4 - - + +
417A TYR* 1.3 78.7 - - - +
419A SER* 1.3 59.2 + - - +
429A ARG* 3.9 21.8 - - + +
430A ASN 3.2 14.6 - - - +
431A LEU* 4.2 11.0 - - + -
457A TYR* 3.7 19.1 - - + +
458A SER* 3.9 16.4 - - - -
459A VAL* 4.1 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A TRP* 3.5 18.7 - - - -
403A GLU 3.2 17.0 - - - -
404A VAL* 4.0 1.3 - - - -
405A ILE* 3.8 8.1 - - - -
417A TYR* 3.7 10.7 - - - -
418A ILE* 1.3 77.2 - - - +
420A ASN* 1.3 58.4 + - - +
421A GLU* 3.1 17.5 + - - +
422A TYR* 5.1 0.5 + - - +
428A GLY 4.3 0.9 - - - -
429A ARG* 3.5 1.8 - - - -
430A ASN* 3.0 29.7 + - - +
432A TYR* 3.2 20.1 - - - -
----------------------------------------------------------
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