Contacts of the strand formed by residues 166 - 175 (chain A) in PDB entry 3NTV
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 166 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 4.6 0.9 - - - -
143A TYR* 3.4 17.0 - - - +
144A ASP 3.6 24.7 - - - +
145A MSE 3.6 9.9 - - - +
146A ILE* 3.9 15.5 - - + -
162A TYR 3.9 0.4 + - - -
163A THR* 2.9 13.3 + - + +
164A PRO 4.4 1.6 - - - +
165A LEU* 1.3 79.6 - - - +
167A LYS* 1.3 67.8 + - - +
170A GLY* 3.9 10.3 - - - +
171A LEU 3.8 15.0 - - - +
172A VAL* 3.6 31.2 - - + -
214A TYR* 4.5 2.9 - - + +
230A LYS* 2.8 42.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN 4.8 10.9 + - - -
71A ASN 5.4 2.2 + - - -
142A VAL* 3.7 21.4 - - + +
143A TYR 2.9 18.5 + - - +
144A ASP* 3.2 34.3 + - - +
165A LEU 3.9 0.8 + - - -
166A LEU* 1.3 79.3 - - - +
168A HIS* 1.4 70.5 + - - +
169A GLN* 3.4 4.0 + - - -
170A GLY* 2.9 32.9 + - - +
230A LYS* 3.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU 3.8 0.4 + - - -
167A LYS* 1.4 85.3 - - - +
169A GLN* 1.3 97.0 + - + +
170A GLY 3.3 2.3 + - - -
230A LYS* 3.9 10.8 - - - +
231A GLY* 3.2 38.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 4.8 6.6 - - - +
167A LYS* 4.8 5.9 - - - -
168A HIS* 1.3 100.2 + - + +
170A GLY* 1.3 64.0 + - - +
171A LEU* 4.3 6.4 - - - +
229A ILE* 4.0 16.8 - - + +
230A LYS 2.7 21.4 + - - +
68B ARG 4.9 5.5 + - - -
71B ASN* 4.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP 3.4 13.2 - - - -
166A LEU* 3.9 10.8 - - - -
167A LYS* 2.9 29.0 + - - -
168A HIS 3.1 2.0 + - - -
169A GLN* 1.3 80.7 - - - +
171A LEU* 1.3 60.4 + - - -
229A ILE* 3.6 2.4 - - - -
230A LYS* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.2 5.8 - - + -
70A ASN* 3.6 31.0 - - + +
72A VAL* 5.0 1.6 - - + -
144A ASP 3.0 12.1 + - - +
145A MSE 3.1 28.8 - - + +
146A ILE 2.9 24.9 + - - +
166A LEU* 3.8 4.0 - - - +
169A GLN 4.3 6.3 - - - +
170A GLY* 1.3 78.0 - - - +
172A VAL* 1.3 63.3 + - - +
173A ILE* 4.1 15.9 - - + -
227A ILE* 4.6 1.6 - - + -
228A SER 3.3 4.9 - - - +
229A ILE* 3.8 22.0 - - + -
69B MSE 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.4 13.0 - - + +
148A ILE* 4.0 17.9 - - + -
159A PHE* 3.8 32.5 - - + -
163A THR* 3.8 20.2 - - + -
166A LEU* 3.6 23.8 - - + +
171A LEU* 1.3 71.2 - - - +
173A ILE* 1.3 65.1 + - - +
174A THR* 4.0 12.1 + - - +
214A TYR* 4.0 8.5 - - + -
226A ALA 3.8 0.9 - - - +
227A ILE* 3.7 2.3 - - - -
228A SER* 2.8 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.8 22.9 - - + -
66A LEU* 3.9 25.1 - - + -
145A MSE 3.9 29.6 - - + -
146A ILE 2.8 10.7 + - - +
147A PHE* 3.4 14.9 - - + -
148A ILE* 2.9 27.2 + - - +
171A LEU* 4.1 12.6 - - + -
172A VAL* 1.3 79.4 - - - +
174A THR* 1.3 62.0 + - - +
225A LEU* 3.6 27.4 - - + -
226A ALA 3.5 3.4 - - - +
227A ILE* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.3 7.4 - - + +
149A ASP 4.4 0.9 - - - -
150A ALA* 3.6 25.8 - - + +
172A VAL* 4.0 10.9 + - - +
173A ILE* 1.3 73.2 - - - +
175A ASP* 1.3 65.2 + - - +
177A VAL* 3.7 10.7 - - + +
204A TYR* 2.7 46.4 + - + +
208A LEU* 4.5 5.7 - - - +
225A LEU* 3.4 7.4 - - - +
226A ALA* 2.8 44.2 + - - +
228A SER* 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.4 22.2 - - - +
56A ASP* 5.2 1.6 + - - +
59A THR* 4.2 17.8 + - - +
147A PHE* 3.9 18.5 - - + -
148A ILE 2.8 13.2 + - - +
149A ASP* 3.6 9.7 - - + +
150A ALA 2.9 25.3 + - - -
173A ILE 4.0 0.6 + - - -
174A THR* 1.3 75.7 - - - +
176A ASN* 1.3 79.0 + - + +
177A VAL 3.3 1.9 + - - -
222A ASP* 5.8 0.2 - - - +
223A ASP* 4.2 15.5 + - - +
224A GLY 3.3 9.9 - - - +
225A LEU* 4.0 7.3 - - + +
----------------------------------------------------------
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