Contacts of the strand formed by residues 176 - 184 (chain A) in PDB entry 1JVN
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 GLU 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG 4.6 0.5 - - - +
112A PHE* 3.4 15.9 - - + -
113A ASP* 2.8 30.9 + - + +
116A GLU* 4.1 3.4 - - - +
117A LYS* 2.7 28.1 + - - +
152A ILE* 3.5 35.8 - - + +
172A LYS* 3.2 5.1 - - - -
173A TYR 2.9 37.4 + - - +
175A SER* 1.3 82.9 - - - +
177A GLU* 1.3 61.2 + - - +
178A PHE* 4.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 4.0 18.4 - - + +
152A ILE* 3.5 7.7 - - - +
153A LEU* 2.7 45.7 + - + +
158A LYS* 2.5 36.6 + - - +
170A LYS* 3.6 21.7 - - + +
171A ALA 3.4 11.9 - - - +
172A LYS* 4.3 11.4 - - + +
175A SER 3.9 3.1 + - - +
176A GLU* 1.3 72.7 - - - +
178A PHE* 1.3 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.7 24.0 - + + -
121A GLU* 3.3 22.2 - - - -
125A ASN* 4.4 1.8 - - - -
145A PHE* 3.7 24.9 - + - -
147A HIS* 3.7 13.2 - + - -
150A ALA* 3.9 23.6 - - + -
151A ALA 3.3 15.7 - - - +
152A ILE* 4.1 2.7 - - - -
153A LEU* 3.8 8.3 - - - +
170A LYS* 3.5 4.7 - - - +
171A ALA* 2.8 66.8 + - + +
172A LYS 4.0 1.6 - - - -
173A TYR* 3.9 13.2 - - + -
176A GLU 4.0 7.0 - - - -
177A GLU* 1.3 74.9 - - - +
179A ILE* 1.3 74.3 + - - +
191A GLN* 4.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.6 7.7 - - + +
90A PHE* 3.9 17.5 - - + -
105A ILE* 4.9 0.9 - - + -
107A PHE* 4.2 1.6 - - + -
151A ALA* 3.0 33.9 + - + +
153A LEU* 3.6 29.2 - - + -
161A LEU* 4.0 16.8 - - + -
168A ILE* 3.8 16.8 - - + -
169A ALA 3.9 3.1 - - - -
178A PHE* 1.3 79.1 - - - +
180A ALA* 1.3 57.7 - - - +
181A ALA* 3.5 15.9 - - - +
182A VAL* 3.3 26.0 - - + -
191A GLN* 3.3 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A CYS* 4.2 16.4 - - - -
145A PHE* 4.0 18.2 - - + -
169A ALA 2.7 19.5 + - - +
170A LYS 4.1 1.1 - - - -
171A ALA* 3.8 23.6 - - + -
178A PHE* 3.4 2.7 + - - -
179A ILE* 1.3 73.6 - - - +
181A ALA* 1.3 58.5 + - - +
190A THR* 3.5 1.2 - - - -
191A GLN* 2.6 34.6 + - - +
192A PHE* 3.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.2 2.0 - - - -
134A PHE* 3.8 7.6 - - + -
137A LEU* 3.8 29.2 - - + -
168A ILE* 3.7 0.7 - - - -
169A ALA* 2.8 27.2 + - + -
179A ILE* 3.4 10.5 - - - +
180A ALA* 1.3 83.6 - - - +
182A VAL* 1.3 63.2 + - - +
189A ALA 3.1 15.3 - - - +
190A THR* 4.1 11.2 - - + -
192A PHE* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.7 4.5 - - + -
89A LEU* 4.0 11.2 - - + -
90A PHE* 4.5 3.1 - - + -
105A ILE* 4.0 16.4 - - + -
134A PHE* 3.7 2.2 - - - -
166A TRP* 3.8 24.0 - - + -
167A LYS 3.5 6.5 - - - -
168A ILE* 3.5 15.0 - - + -
179A ILE* 3.3 28.9 - - + -
181A ALA* 1.3 71.6 - - - +
183A ASN* 1.3 64.3 + - - +
187A ILE* 4.4 1.1 - - + -
188A PHE* 3.4 9.4 - - - -
189A ALA* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.6 40.1 - - + +
135A PHE* 3.7 26.7 - - - -
166A TRP* 3.8 1.9 - - - -
167A LYS* 2.7 48.8 + - + +
182A VAL* 1.3 78.1 - - - +
184A LYS* 1.3 64.5 + - - +
185A ASN 3.8 14.5 + - - +
186A ASN 5.1 0.2 - - - -
187A ILE 2.8 21.4 + - - -
188A PHE* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 2.8 28.8 + - - +
165A GLY* 3.6 16.8 - - - +
166A TRP* 3.4 50.8 - - + +
167A LYS* 5.8 0.2 - - - -
183A ASN* 1.3 76.9 - - - +
185A ASN* 1.3 91.1 + - - +
186A ASN 3.1 0.9 + - - -
187A ILE* 2.9 28.5 + - + +
----------------------------------------------------------
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