Contacts of the strand formed by residues 162 - 167 (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 ARG 162 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M TRP* 3.1 23.3 + - + -
126M VAL* 5.6 2.1 - - - +
135M GLN* 3.5 30.4 + - - +
136M TYR* 3.1 35.2 + - - +
137M ASP* 2.9 28.1 + - - -
154M TYR* 3.6 52.5 - - + +
155M LYS 3.6 6.3 - - - +
156M THR* 5.8 0.9 - - - -
160M GLY 5.3 0.2 - - - +
161M THR* 1.3 75.2 + - - +
163M ILE* 1.3 59.9 + - - +
164M GLY 3.7 0.2 - - - -
187M ARG* 3.6 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123M SER* 3.8 2.3 - - - -
124M TRP* 2.9 62.3 + - - +
125M ALA* 4.6 8.1 - - + -
126M VAL* 5.1 7.4 - - + +
155M LYS* 3.1 18.6 + - + +
156M THR 4.1 15.5 - - - +
157M ASP* 4.4 23.3 - - + +
161M THR 3.8 0.8 + - - -
162M ARG* 1.3 73.7 - - - +
164M GLY* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122M CYS 3.3 12.3 - - - -
123M SER* 4.1 3.8 - - - -
124M TRP* 3.5 15.0 - - - -
154M TYR* 3.6 8.7 - - - +
155M LYS* 3.2 28.1 + - - +
162M ARG 3.7 0.4 - - - -
163M ILE* 1.3 84.5 + - - +
165M CYS* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 165 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M SER* 3.4 3.5 - - - -
122M CYS* 2.9 30.9 + - + +
124M TRP* 4.2 2.5 - - + -
138M LEU* 4.0 21.3 - - + -
151M CYS* 2.0 49.6 - - + -
153M HIS 3.8 8.7 - - - -
154M TYR* 4.3 1.1 - - + +
155M LYS* 4.4 9.0 + - - +
164M GLY* 1.3 76.3 - - - +
166M ARG* 1.3 73.5 + - - +
167M PHE* 3.8 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M HIS* 4.3 7.9 - - - +
119M PHE* 3.7 25.9 - - + -
120M LEU 3.4 5.6 - - - +
121M SER* 3.2 22.4 - - - +
151M CYS* 4.8 0.6 - - - -
153M HIS* 3.4 46.3 + - - +
155M LYS* 4.0 23.7 - - - +
165M CYS* 1.3 83.9 - - - +
167M PHE* 1.3 70.3 + - - +
168M ASP* 2.8 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 167 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M PHE* 3.8 6.2 - - - -
120M LEU* 2.7 48.8 + - + +
122M CYS* 5.5 4.3 - - - -
138M LEU* 3.6 33.9 - - + -
140M LEU* 3.8 31.0 - - + -
149M TYR* 4.3 9.6 - - + -
150M GLU 4.2 17.7 - - - -
151M CYS* 4.1 13.2 - - - -
152M LEU 5.8 1.1 - - - +
165M CYS* 3.8 12.6 - - - -
166M ARG* 1.3 79.4 - - - +
168M ASP* 1.3 63.0 + - - +
169M ASP 3.8 1.8 - - - +
170M ILE* 4.6 8.5 - - + -
173M LEU* 3.5 29.6 - - + -
----------------------------------------------------------
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