Contacts of the strand formed by residues 331 - 336 (chain D) in PDB entry 1M7X
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 ASN 331 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ARG* 2.6 53.1 - - - +
236D ALA* 3.7 16.7 - - - +
237D ASN* 2.8 16.7 + - - -
282D THR 2.9 7.3 + - - -
283D HIS* 3.3 25.8 - - + +
284D LEU* 2.9 26.5 + - - +
329D GLY 5.4 1.4 + - - -
330D LEU* 1.3 78.0 - - - +
332D VAL* 1.3 62.1 + - - +
400D ASP* 3.1 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D LEU* 3.3 15.0 - - + +
286D LEU* 4.3 16.6 - - + -
321D PHE* 5.3 1.3 - - + -
322D ILE* 3.9 27.8 - - + -
325D ALA* 3.6 31.2 - - + -
326D HIS* 4.2 9.9 - - + +
331D ASN* 1.3 78.3 - - - +
333D ILE* 1.3 71.4 + - - +
334D LEU* 5.5 0.2 - - + -
399D ILE* 3.8 11.6 - - + -
400D ASP* 2.7 43.3 + - - +
401D ALA 3.1 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ILE* 3.5 30.3 - - + -
283D HIS* 3.2 45.1 - - + +
284D LEU 2.6 10.9 + - - +
285D GLU* 3.1 20.1 - - + +
286D LEU* 2.9 29.3 + - - +
331D ASN* 5.6 0.2 - - + -
332D VAL* 1.3 76.1 - - - +
334D LEU* 1.3 63.0 + - - +
401D ALA* 3.3 27.8 - - + +
402D LEU 4.4 0.7 - - - -
403D ARG* 4.0 20.4 - - + +
456D MET* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D LEU* 4.0 16.8 - - + +
287D LEU 4.2 0.7 - - - +
289D ILE* 3.4 36.3 - - + +
290D ASN* 6.1 1.3 - - - +
318D PHE* 5.4 1.1 - - + -
332D VAL* 4.1 2.2 + - + -
333D ILE* 1.3 74.3 - - - +
335D ASP* 1.3 82.5 + - - +
336D TRP* 2.9 6.2 + - - +
393D TRP* 3.6 52.7 - - + +
399D ILE* 4.3 16.8 - - + -
401D ALA 2.8 13.9 + - - +
402D LEU* 3.4 12.3 - - + +
403D ARG* 3.0 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D GLU* 5.0 0.5 - - - +
285D GLU* 3.2 13.2 - - - +
286D LEU 3.0 24.3 + - - +
287D LEU* 3.8 7.7 - - - +
288D PRO* 3.6 28.1 - - + +
290D ASN* 5.4 3.1 + - - -
300D TYR* 2.4 31.4 + - + -
333D ILE 4.0 0.2 + - - -
334D LEU* 1.3 82.3 - - - +
336D TRP* 1.3 61.9 + - - +
337D VAL* 4.1 1.7 + - + -
403D ARG* 2.7 43.3 + - - +
405D ASP* 5.7 0.4 - - - +
525D HIS* 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ASN* 6.0 2.9 - - - +
305D LEU* 5.3 3.0 - - + +
334D LEU* 2.9 9.3 + - + +
335D ASP* 1.3 73.4 - - - +
337D VAL* 1.3 65.2 + - - +
338D PRO* 3.0 44.2 - - + +
386D LEU* 2.9 34.9 - - + +
389D ASN* 2.8 31.3 + - - +
390D ALA* 3.7 13.3 - - + +
393D TRP* 4.2 15.3 - + - -
402D LEU* 4.0 28.3 - - + -
403D ARG 2.7 20.3 + - - +
404D VAL* 3.5 32.3 - - + -
405D ASP* 4.0 1.9 - - - +
438D PHE* 4.5 5.6 - + - -
439D LEU* 6.2 1.6 - - + -
442D THR* 3.7 32.8 - - + -
446D LEU* 5.4 0.7 - - + -
455D THR* 6.3 1.6 - - + -
----------------------------------------------------------
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