Contacts of the strand formed by residues 277 - 285 (chain D) in PDB entry 4GJ0
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 LEU 277 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D GLY 3.4 1.2 - - - +
181D THR* 3.2 3.7 - - - -
182D LYS* 2.9 31.6 + - - +
217D THR 5.5 2.9 - - - +
218D GLY 4.3 3.8 - - - +
219D SER 3.9 2.0 - - - +
220D TRP* 3.5 55.4 - - + +
261D MET* 3.6 43.1 - - + -
275D ARG* 3.6 28.9 + - + +
276D LYS* 1.3 79.8 - - - +
278D GLY* 1.3 61.8 + - - +
279D ALA 3.2 10.4 + - - +
280D TRP* 4.7 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D LYS* 3.4 6.9 - - - +
180D GLY 3.1 28.1 + - - -
181D THR* 4.3 13.2 - - - +
215D SER* 5.6 0.4 - - - -
217D THR* 5.5 9.5 - - - +
218D GLY 4.4 3.2 + - - -
277D LEU* 1.3 73.0 - - - +
279D ALA* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D GLY 3.4 13.9 - - - +
179D LYS* 5.1 2.5 - - + -
215D SER* 3.5 21.8 - - - +
218D GLY 3.4 10.4 + - - +
219D SER* 3.1 23.8 - - - +
220D TRP* 2.9 18.5 + - - -
277D LEU* 3.2 9.0 + - - +
278D GLY* 1.3 81.8 - - - +
280D TRP* 1.3 69.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D TYR* 3.9 14.8 - + - -
177D PHE* 3.9 0.2 - - - -
178D GLY* 2.8 50.5 + - - +
179D LYS 3.7 17.2 - - - -
180D GLY 3.0 26.6 + - - -
182D LYS* 3.3 34.4 - - + +
187D ALA* 3.6 25.1 - - + -
190D ALA* 4.0 19.3 - - + -
191D CYS* 4.2 4.0 - - - -
194D MET* 4.2 7.9 - - + -
198D LEU* 4.4 2.9 - - + -
219D SER* 3.9 1.1 - - - -
220D TRP* 3.5 15.7 - + + +
277D LEU 4.7 0.9 - - - -
279D ALA* 1.3 85.4 - - - +
281D VAL* 1.3 65.8 + - - +
282D CYS* 3.8 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D TYR* 4.6 1.6 - - + -
176D TYR 3.4 11.4 - - - +
177D PHE* 3.8 35.7 - - + -
191D CYS* 4.2 0.4 - - - -
198D LEU* 3.3 10.0 - - - +
199D VAL* 2.8 49.0 + - + +
210D LEU* 4.2 10.5 - - + -
214D ALA* 5.6 1.1 - - + -
219D SER* 4.1 18.6 - - - +
220D TRP 3.1 7.8 + - - +
262D MET* 4.2 14.4 - - + -
279D ALA* 6.2 0.2 - - + -
280D TRP* 1.3 79.0 - - - +
282D CYS* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D TRP* 3.7 20.2 - - + -
175D TYR* 3.4 4.0 - - - -
176D TYR* 3.0 31.7 + - + +
191D CYS* 2.1 52.9 - - + -
194D MET* 4.0 9.4 - - - -
197D GLN 2.9 8.7 - - - +
199D VAL 4.4 0.9 - - - -
280D TRP* 3.8 21.3 - - - -
281D VAL* 1.3 80.2 - - - +
283D ASP* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D TRP* 3.8 2.9 - - - -
173D LYS* 2.8 38.0 + - - -
174D CYS 3.1 12.3 - - - +
175D TYR* 3.9 10.3 - - + -
196D GLY* 3.3 1.7 - - - -
197D GLN* 2.7 41.0 + - - +
198D LEU 4.3 0.9 - - - +
199D VAL* 3.6 10.1 - - + +
200D SER* 3.1 19.6 + - - -
282D CYS* 1.3 75.3 - - - +
284D ARG* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D PRO* 3.5 30.9 - - - +
167D TRP* 3.7 34.3 - - + +
173D LYS* 3.5 7.8 - - - +
174D CYS* 2.8 38.9 + - + -
194D MET 2.9 22.0 + - - -
195D GLU* 3.4 39.9 + - - +
196D GLY* 4.3 0.7 - - - -
283D ASP* 1.3 78.1 - - - +
285D LEU* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D PRO* 5.6 1.6 - - - +
172D ARG* 3.9 12.6 - - + +
173D LYS* 4.6 7.9 - - + +
174D CYS* 4.0 3.0 - - - -
284D ARG* 1.3 86.7 + - - +
286D ALA* 1.3 68.9 + - - +
287D THR* 3.9 7.2 + - + +
----------------------------------------------------------
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