Contacts of the strand formed by residues 408 - 416 (chain A) in PDB entry 1ATT
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 PRO 408 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.5 7.9 - - + -
241A TYR 3.7 9.6 - - - +
242A LYS 4.1 0.2 - - - -
243A ALA* 3.5 25.1 - - + +
286A LEU* 4.0 2.6 - - - +
287A PRO* 4.0 14.9 - - - +
293A LEU* 4.3 14.7 - - + +
407A ARG* 1.4 91.8 + - + +
409A PHE* 1.3 61.1 + - - +
426A ARG* 4.9 6.7 - - + -
427A VAL 3.4 12.8 - - - +
428A ALA* 3.4 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 4.0 14.6 - + - -
284A LEU* 4.0 28.5 - - + -
285A ILE 3.3 17.7 - - - +
286A LEU* 3.9 10.8 - - + -
293A LEU* 4.2 8.9 - - - +
321A MET* 5.1 1.6 - - + -
322A PRO* 4.1 9.6 - - + -
324A PHE* 4.1 18.2 - + - -
405A ALA* 3.8 24.7 - - + -
407A ARG 3.1 22.0 - - - -
408A PRO* 1.3 75.9 - - + +
410A LEU* 1.3 70.3 + - - +
411A VAL* 4.1 12.1 - - + -
426A ARG* 3.5 3.4 - - - +
427A VAL* 3.1 52.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 4.5 12.1 - - + +
284A LEU* 3.5 4.7 - - - -
285A ILE* 3.0 60.6 + - + -
293A LEU* 3.5 39.5 - - + -
296A VAL* 4.0 11.4 - - + -
297A GLU* 4.6 3.4 - - + -
300A LEU* 3.8 28.3 - - + -
409A PHE* 1.3 78.5 - - - +
411A VAL* 1.3 61.6 + - - +
412A LEU* 4.4 18.6 - - + -
424A MET* 4.6 8.3 - - + -
425A GLY 3.3 15.3 - - - +
426A ARG* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 4.9 3.4 - - + -
282A MET* 4.0 24.5 - - + -
283A VAL 3.5 3.8 - - - -
284A LEU* 4.5 3.1 - - + -
324A PHE* 5.1 2.9 - - + -
326A ILE* 6.1 0.7 - - + -
374A LEU* 4.6 17.5 - - + -
409A PHE* 4.1 24.9 - - + +
410A LEU* 1.3 79.0 - - - +
412A LEU* 1.3 77.3 + - - +
413A ILE* 4.2 11.0 - - + -
424A MET* 3.3 6.1 - - - +
425A GLY* 2.9 33.9 + - - +
427A VAL* 4.6 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A MET* 3.5 1.7 - - - -
283A VAL* 2.9 45.0 + - + +
285A ILE* 4.2 21.8 - - + -
300A LEU* 6.1 1.1 - - + -
308A TRP* 3.6 39.3 - - + +
410A LEU* 4.4 13.7 - - + -
411A VAL* 1.3 78.8 - - - +
413A ILE* 1.3 68.7 + - - +
414A ARG* 4.0 5.6 - - + +
421A ILE* 3.7 38.1 - - + -
423A PHE 3.8 5.2 - - - +
424A MET* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 4.4 2.9 - - + -
222A PHE* 4.6 17.3 - - + -
275A PHE* 4.8 0.4 - - + -
280A ILE* 4.1 15.3 - - + -
281A THR 3.5 15.3 - - - +
282A MET* 3.9 24.5 - - + -
374A LEU* 4.1 18.2 - - + -
383A ALA* 4.4 8.3 - - + -
411A VAL* 4.2 9.0 - - + -
412A LEU* 1.3 79.3 - - - +
414A ARG* 1.3 61.1 + - - +
421A ILE* 4.9 1.1 - - - +
422A ILE* 3.1 29.2 + - + +
423A PHE* 3.3 42.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 6.2 0.4 - - - -
272A GLU* 4.2 9.0 - - - -
280A ILE* 3.3 7.3 - - - +
281A THR* 3.0 34.8 + - - +
283A VAL* 4.0 15.9 - - + -
305A LEU* 3.8 16.6 - - - +
308A TRP* 3.1 59.4 - - - +
412A LEU* 4.0 9.3 - - + -
413A ILE* 1.3 75.1 - - - +
415A GLU* 1.3 60.5 + - - +
416A VAL* 3.6 11.9 - - + +
419A ASN* 2.7 45.4 + - - +
420A THR 3.8 8.5 - - - +
421A ILE* 4.3 21.6 - - + +
422A ILE* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG 5.3 1.3 - - - -
131A LEU* 3.6 19.0 - - + +
141A LEU* 4.5 3.6 - - + -
279A ASP* 3.3 35.2 - - - +
280A ILE* 4.0 16.6 - - + +
414A ARG* 1.3 71.0 - - - +
416A VAL* 1.3 53.1 + - - +
417A ALA* 3.7 6.2 - - - +
418A LEU* 3.0 31.3 + - - +
419A ASN* 2.7 31.2 + - - -
420A THR* 3.4 18.9 + - - +
422A ILE* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TRP* 5.3 0.7 - - - -
260A ARG* 5.1 9.9 - - - +
272A GLU* 4.6 8.1 - - - +
278A ASP* 4.4 10.5 - - - +
279A ASP 2.9 17.2 + - - +
281A THR* 3.6 36.1 - - + +
414A ARG* 4.7 10.3 - - + +
415A GLU* 1.3 70.7 - - - +
417A ALA* 1.3 66.7 + - - +
419A ASN* 3.1 17.9 + - - +
----------------------------------------------------------
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