Contacts of the strand formed by residues 388 - 395 (chain D) in PDB entry 2W8B
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 MET 388 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ASN 3.6 15.9 - - - +
65D SER* 3.2 30.7 - - - +
382D LEU* 3.5 8.1 - - - +
383D ALA* 2.9 32.9 + - + +
386D GLY 3.6 0.6 - - - -
387D THR* 1.3 90.7 + - - +
389D VAL* 1.3 64.6 + - - +
403D LEU* 4.1 9.6 - - + -
404D VAL 3.7 26.9 - - - +
405D SER* 3.7 10.3 - - - +
406D THR* 3.9 0.8 - - - +
410D PHE* 4.0 17.0 - - + -
426D TRP* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 389 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D VAL* 4.0 13.9 - - + -
358D ILE* 4.5 7.0 - - + -
371D LEU* 4.4 9.0 - - + -
380D PRO* 3.8 23.6 - - + -
381D SER 3.6 9.0 - - - +
382D LEU* 3.8 11.0 - - + -
388D MET* 1.3 78.3 - - - +
390D ILE* 1.3 74.2 + - - +
391D TYR* 4.5 5.5 - - + -
402D ASN 3.8 0.2 - - - +
403D LEU* 3.2 8.3 - - - +
404D VAL* 2.7 46.8 + - + +
406D THR* 3.7 21.5 - - + -
426D TRP* 4.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 3.9 28.9 - - + -
379D THR 3.8 1.4 - - - +
380D PRO* 3.5 0.3 - - - +
381D SER* 2.9 54.9 + - - +
389D VAL* 1.3 73.3 - - - +
391D TYR* 1.3 68.3 + - - +
401D LEU* 4.3 5.8 - - + -
402D ASN 3.3 11.2 - - - +
403D LEU* 3.8 8.7 - - + -
414D LEU* 3.6 26.7 - - + -
424D PRO* 3.8 27.8 - - + -
425D ALA 4.7 0.2 - - - +
426D TRP* 3.7 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 391 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D ILE* 3.6 23.8 - - + -
372D SER* 3.3 14.5 - - - -
374D THR* 2.6 25.5 + - - +
377D ASP* 3.1 26.9 - - + -
378D GLU 3.4 11.4 - - - +
379D THR 3.8 0.9 - - - -
380D PRO* 3.8 11.9 - - + -
389D VAL* 4.5 2.7 - - + -
390D ILE* 1.3 77.6 - - - +
392D SER* 1.3 79.8 + - - +
393D SER* 4.3 0.2 - - - -
401D LEU* 3.4 6.1 - - - +
402D ASN* 2.8 65.5 + - + +
403D LEU 4.4 1.2 + - - -
404D VAL* 3.8 32.0 - - + +
424D PRO* 3.7 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 392 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D LEU 3.6 1.2 - - - +
377D ASP* 3.4 2.9 - - - -
378D GLU* 2.9 43.0 + - - +
379D THR* 3.9 15.2 + - - -
391D TYR* 1.3 81.3 - - - +
393D SER* 1.3 63.5 + - - +
399D SER* 4.0 3.3 + - - -
400D VAL 2.9 17.0 + - - -
401D LEU* 4.5 0.4 - - - -
402D ASN* 4.0 0.2 - - - -
421D VAL 3.5 13.0 + - - -
422D LYS* 3.5 11.5 - - - +
424D PRO* 4.1 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 393 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D THR* 4.0 9.5 - - - -
375D PHE 3.0 17.3 - - - -
376D LEU 3.6 6.5 - - - -
377D ASP* 3.4 17.7 - - - -
378D GLU* 5.6 0.2 - - - -
392D SER* 1.3 74.1 + - - +
394D SER* 1.3 67.3 + - - +
395D GLN* 5.1 2.1 + - - +
399D SER* 3.3 7.0 - - - -
400D VAL* 2.9 34.8 + - - +
402D ASN* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 394 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D PHE* 2.8 49.2 + - - +
376D LEU* 3.7 19.1 + - - +
393D SER* 1.3 79.5 + - - +
395D GLN* 1.3 63.6 + - - +
396D GLY 4.5 0.2 - - - -
398D GLY 3.5 10.0 + - - -
399D SER* 4.5 7.4 + - - -
111E GLU* 4.2 5.2 + - - -
158E HIS* 4.1 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 395 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D SER* 4.2 2.2 + - - +
394D SER* 1.3 74.1 - - - +
396D GLY* 1.3 68.2 + - - +
397D MET 3.2 2.1 + - - -
398D GLY 3.1 15.7 + - - +
400D VAL* 3.8 36.8 - - + +
402D ASN* 5.1 1.2 - - - +
413D ARG* 3.5 32.1 + - - +
----------------------------------------------------------
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