Contacts of the strand formed by residues 191 - 205 (chain M) in PDB entry 2VGL
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 VAL 191 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M ARG* 5.1 10.1 - - - +
183M LEU* 3.9 7.0 - - + -
184M LEU 4.0 2.5 - - - -
185M MET* 3.4 14.9 - - + +
189M GLY 3.5 1.5 + - - +
190M GLN* 1.3 76.8 + - - +
192M LEU* 1.3 60.9 + - - +
193M SER* 4.0 6.3 - - - -
194M ALA* 3.8 30.5 - - + +
285M LEU* 3.4 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184M LEU* 2.8 19.2 + - + +
185M MET 4.1 3.8 - - - -
186M SER* 3.9 21.5 - - - +
190M GLN* 2.8 29.4 + - + +
191M VAL* 1.3 72.0 - - - +
193M SER* 1.3 64.1 + - - +
434M ARG* 3.9 30.5 - - - +
51S GLU* 3.7 35.7 - - + +
52S PHE* 4.2 0.7 - - - +
53S ARG* 3.3 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183M LEU* 3.6 2.1 - - - +
184M LEU* 2.8 46.7 + - - +
191M VAL* 3.5 4.7 - - - -
192M LEU* 1.3 80.2 - - - +
194M ALA* 1.3 60.8 + - - +
53S ARG* 3.6 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182M ASN 3.1 16.4 - - - +
183M LEU* 4.2 6.1 - - + -
191M VAL* 3.8 18.5 - - + +
193M SER* 1.3 77.6 - - - +
195M HIS* 1.3 68.6 + - - +
280M THR* 3.9 15.7 - - - +
283M ILE* 3.7 20.3 - - + +
285M LEU* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182M ASN* 2.7 69.4 + - + +
194M ALA* 1.3 79.4 - - - +
196M VAL* 1.3 62.3 - - - +
197M SER* 4.2 5.8 + - - -
242M ALA* 3.8 26.6 - - + +
278M ARG* 4.0 25.4 + - + -
279M THR 3.3 11.7 - - - +
280M THR* 3.8 3.1 - - + -
283M ILE* 3.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179M GLU* 3.7 27.1 - - + +
180M SER 3.2 9.4 - - - +
181M VAL* 3.6 32.1 - - + -
195M HIS* 1.3 74.4 - - - +
197M SER* 1.3 75.5 + - - +
198M GLY 4.3 0.9 - - - +
277M TYR* 4.8 1.6 - - + -
278M ARG* 3.3 7.1 - - - +
279M THR* 2.7 49.1 + - + -
283M ILE* 3.7 10.4 - - + +
396M PRO* 3.9 13.2 - - + -
397M SER* 3.9 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 197 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178M LEU 3.9 0.2 - - - +
179M GLU* 3.4 1.4 - - - -
180M SER* 2.7 47.1 + - - -
182M ASN* 5.1 2.2 - - - -
195M HIS* 4.2 7.9 + - - -
196M VAL* 1.3 76.4 - - - +
198M GLY* 1.3 58.2 + - - +
277M TYR 3.6 5.0 + - - -
278M ARG* 3.2 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178M LEU 3.3 10.1 - - - -
179M GLU* 4.2 1.8 - - - -
197M SER* 1.3 76.0 - - - +
199M ARG* 1.3 67.7 + - - +
276M ARG* 3.6 6.3 + - - +
277M TYR* 2.9 54.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176M ASP 3.5 0.9 - - - +
177M VAL* 3.6 2.9 - - - -
178M LEU* 3.0 61.5 + - + +
198M GLY* 1.3 77.2 - - - +
200M VAL* 1.3 64.5 + - - +
201M VAL* 3.9 19.2 - - + +
273M GLU* 3.9 29.2 + - + +
275M MET 3.1 14.8 - - - +
276M ARG* 4.0 25.8 - - + +
277M TYR* 3.3 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175M LEU* 4.1 26.0 - - + -
176M ASP 3.4 5.4 - - - +
177M VAL* 4.1 19.1 - - + -
199M ARG* 1.3 75.9 - - - +
201M VAL* 1.3 71.9 + - - +
214M PHE* 4.7 12.3 - - + -
273M GLU* 3.8 1.6 - - - -
274M LEU* 3.0 41.4 + - + +
275M MET* 3.0 35.3 + - + +
277M TYR* 4.6 0.7 - - + -
399M LEU* 4.1 14.8 - - + -
401M VAL* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M PHE 3.9 0.3 - - - +
175M LEU* 3.4 3.6 - - - -
176M ASP* 2.8 43.0 + - + +
178M LEU* 3.7 27.8 - - + -
199M ARG* 3.9 27.6 - - + +
200M VAL* 1.3 76.0 - - - +
202M MET* 1.3 64.9 + - - +
203M LYS* 5.8 0.4 - - + -
271M GLU* 3.6 32.3 - - + +
272M PHE 3.5 13.2 - - - +
273M GLU* 4.5 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 202 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M LEU* 4.4 10.3 - - + -
174M PHE 3.5 5.4 - - - +
175M LEU* 3.5 27.4 - - + -
200M VAL 3.7 0.8 + - - -
201M VAL* 1.3 76.7 - - - +
203M LYS* 1.3 61.9 + - - +
204M SER* 3.5 29.6 - - - +
206M LEU* 4.9 0.9 - - + -
212M CYS* 4.7 4.7 - - - -
265M PHE* 3.7 31.2 - - + -
267M PRO* 4.1 16.4 - - + -
270M GLY 3.4 2.6 - - - +
271M GLU* 3.2 1.6 - - - +
272M PHE* 2.7 63.6 + - + +
274M LEU* 4.7 8.5 - - + -
404M LEU* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M PHE* 2.7 74.8 + - + -
201M VAL* 4.2 0.9 - - + -
202M MET* 1.3 74.1 - - - +
204M SER* 1.3 60.5 + - - +
205M TYR* 3.5 35.0 + - + +
270M GLY 3.2 7.0 - - - +
271M GLU* 4.0 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M ARG* 4.9 1.6 + - - -
172M GLU 3.6 9.4 - - - -
173M LEU* 4.0 4.3 - - - +
202M MET* 3.5 29.7 - - - +
203M LYS* 1.3 75.2 - - - +
205M TYR* 1.3 64.2 + - - +
206M LEU* 3.9 11.8 - - - +
267M PRO* 4.1 6.6 - - - +
268M PRO 3.5 18.7 + - - -
269M ASP* 3.1 6.4 - - - +
270M GLY 2.9 29.5 + - - -
272M PHE* 5.1 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M TYR* 3.6 47.1 - + + -
170M ARG 3.7 2.8 - - - +
171M ASN* 3.1 6.1 - - - -
172M GLU* 2.6 62.0 + - + +
174M PHE* 4.3 9.6 - + - -
203M LYS* 3.5 41.8 + - + +
204M SER* 1.3 74.5 - - - +
206M LEU* 1.3 57.4 + - - +
269M ASP* 4.2 0.9 - - - -
270M GLY* 3.8 20.2 - - - -
271M GLU* 5.1 0.7 + - - +
----------------------------------------------------------
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