Contacts of the strand formed by residues 192 - 201 (chain M) in PDB entry 6NMY
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 GLY 192 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M GLY* 3.1 28.3 - - - -
102M LYS 3.4 5.4 + - - -
186M GLY 5.4 0.7 - - - -
187M ARG* 6.4 0.2 - - - -
191M PHE* 1.3 72.5 - - - +
193M ILE* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M GLY* 4.9 0.2 - - - -
102M LYS* 4.4 2.9 - - + -
105M ALA* 3.5 40.6 - - + +
106M GLY* 3.8 2.0 - - - -
131M PRO* 4.5 9.2 - - + -
134M VAL* 3.5 25.1 - - + -
136M TYR* 4.3 1.6 - - + -
185M ARG* 5.7 0.5 - - - +
186M GLY* 3.8 37.6 + - - +
187M ARG 4.4 0.2 - - - -
188M SER* 4.0 17.0 - - - -
191M PHE* 4.0 18.1 + - + -
192M GLY* 1.3 77.1 - - - +
194M PRO* 1.3 82.1 - - + +
195M CYS* 3.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 194 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M CYS 5.7 2.9 - - - +
100M SER 4.0 16.6 - - - +
101M GLY* 3.9 3.8 - - - -
102M LYS 3.5 34.8 - - - +
103M PRO* 5.5 1.6 - - + -
104M TRP 5.7 0.7 - - - +
105M ALA 4.9 0.2 - - - +
106M GLY* 3.2 34.3 - - - +
107M ALA 4.4 0.7 + - - -
136M TYR* 5.1 0.5 - - - -
186M GLY* 4.5 3.2 + - - -
192M GLY 3.9 0.2 - - - -
193M ILE* 1.3 94.9 - - + +
195M CYS* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 195 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M LEU* 3.6 11.4 - - - -
76M CYS* 2.0 56.2 - - - +
106M GLY* 4.9 1.4 - - - -
183M LEU* 3.5 12.1 - - + -
184M VAL 3.1 19.1 - - - +
185M ARG* 3.9 13.0 - - + +
193M ILE 3.8 0.6 + - - +
194M PRO* 1.3 78.9 - - - +
196M THR* 1.3 69.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M CYS* 3.6 5.8 - - - -
106M GLY* 4.0 0.7 - - - -
107M ALA* 2.4 50.3 + - - +
108M GLU* 4.8 3.6 - - + -
110M LEU* 4.3 22.1 - - + +
183M LEU* 3.6 1.0 - - - -
184M VAL* 2.9 32.2 + - - +
195M CYS* 1.3 83.6 + - - +
197M ASP* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M SER* 2.9 26.8 + - - -
75M LEU* 3.2 22.8 + - + -
76M CYS* 3.6 18.7 - - - +
77M GLU* 4.4 1.4 + - - +
110M LEU* 4.9 2.2 - - - +
181M HIS* 3.4 26.5 - - - +
182M ILE 3.1 13.5 - - - +
183M LEU* 4.2 4.5 - - + -
196M THR* 1.3 81.8 - - - +
198M LYS* 1.3 67.0 + - - +
199M PHE* 4.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M LEU* 2.6 48.9 + - + +
111M THR* 3.8 14.8 - - - +
112M CYS 4.9 6.0 - - - +
181M HIS* 3.7 2.5 - - - -
182M ILE* 2.9 34.0 + - + +
197M ASP* 1.3 79.7 - - - +
199M PHE* 1.3 76.3 + - - +
200M VAL* 3.8 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I GLY* 5.8 5.8 - - - -
37M GLN* 4.5 5.6 - - - -
71M GLY 4.4 4.9 - - - -
72M ALA* 3.5 44.4 - - + -
73M ILE 3.4 24.2 - - - -
74M SER* 4.1 4.9 - - - -
180M SER 3.6 6.1 - - - +
181M HIS* 3.1 40.4 - + + -
197M ASP* 4.1 7.4 - - - -
198M LYS* 1.3 82.0 - - - +
200M VAL* 1.3 63.6 + - - +
201M VAL* 5.8 0.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
112M CYS* 4.5 11.0 - - + +
179M SER* 3.3 6.1 - - - -
180M SER* 2.9 49.0 + - - +
182M ILE* 3.8 30.7 - - + -
198M LYS* 3.8 24.5 - - + +
199M PHE* 1.3 80.4 - - - +
201M VAL* 1.3 63.3 + - - +
202M PHE* 4.2 6.1 - - + -
205M ILE* 4.2 27.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
45I GLN* 3.5 24.7 - - - +
49I MET* 3.9 25.1 - - + -
113I PHE* 4.2 10.8 - - + -
117I THR* 5.5 3.8 - - + -
178M GLN* 3.4 20.6 - - + +
179M SER* 4.5 2.9 - - - -
200M VAL* 1.3 77.7 - - - +
202M PHE* 1.3 67.9 + - - +
203M SER* 4.1 14.8 - - - +
204M GLN* 3.1 29.5 + - + +
205M ILE* 3.5 17.0 + - - +
----------------------------------------------------------
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