Contacts of the strand formed by residues 172 - 182 (chain A) in PDB entry 1I1N
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 172 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 4.1 5.2 - - - +
152A TYR 3.6 7.6 - - - +
153A ASP 4.8 0.2 - - - +
155A ILE* 3.6 26.7 - - + +
168A LEU 3.6 10.1 - - - +
169A ILE* 3.2 22.4 + - + +
170A ASP 4.3 4.7 - - - +
171A GLN* 1.3 79.4 - - - +
173A LYS* 1.3 63.0 + - - +
174A PRO* 4.6 0.2 - - - +
176A GLY 4.6 1.3 - - - +
177A ARG 3.8 28.0 - - - +
178A LEU* 3.9 18.6 - - + +
194A TYR* 4.2 15.9 - - + +
196A LYS* 3.2 40.3 - - + +
202A ILE* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY 5.3 2.2 + - - -
79A ALA* 5.1 1.2 - - - +
80A LYS* 4.3 10.0 - - - +
151A PRO* 3.4 46.9 - - + -
152A TYR* 2.9 17.3 + - - +
153A ASP* 2.7 44.4 + - - +
172A LEU* 1.3 75.1 - - - +
174A PRO* 1.3 77.2 - - + +
175A GLY 3.2 0.2 + - - -
176A GLY* 2.8 20.8 + - - +
196A LYS* 3.5 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 6.1 0.7 - - + -
153A ASP* 5.4 1.9 - - - +
172A LEU 4.6 1.3 - - - +
173A LYS* 1.3 94.5 - - + +
175A GLY* 1.3 58.3 + - - +
176A GLY 3.3 1.7 + - - -
196A LYS* 4.1 15.5 - - + +
197A LEU 3.8 17.3 - - - +
198A GLN* 4.0 18.8 - - + +
200A GLY* 5.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 3.8 21.0 + - - +
153A ASP* 5.8 1.3 - - - -
174A PRO* 1.3 71.9 - - - +
176A GLY* 1.3 63.8 + - - +
195A ASP* 5.4 0.7 - - - +
196A LYS 2.7 18.1 + - - -
197A LEU* 4.1 4.5 + - - -
198A GLN* 4.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR 4.4 2.9 - - - -
153A ASP* 3.1 22.4 - - - -
172A LEU* 4.2 7.2 - - - -
173A LYS 2.8 18.0 + - - -
174A PRO 3.1 1.6 + - - -
175A GLY* 1.3 83.0 - - - +
177A ARG* 1.3 59.4 + - - +
194A TYR 4.0 0.2 - - - +
195A ASP* 3.5 5.0 - - - +
196A LYS 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 2.8 39.3 + - - +
71A LEU* 3.6 13.6 - - + +
73A ASP* 5.8 2.6 + - - +
74A GLN* 3.6 33.6 + - + +
153A ASP 3.0 6.9 + - - -
154A ALA* 3.5 4.2 - - - -
155A ILE 2.9 25.1 + - - +
172A LEU* 3.8 4.9 - - - +
176A GLY* 1.3 76.3 - - - +
178A LEU* 1.3 62.1 + - - +
179A ILE* 4.2 5.8 - - + -
193A GLN* 3.2 39.6 + - + +
194A TYR 3.3 6.7 - - - +
195A ASP* 2.7 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 3.3 31.2 - - + +
157A VAL* 4.0 19.1 - - + -
164A VAL* 4.5 4.5 - - + -
168A LEU* 4.0 24.0 - - + -
169A ILE* 4.1 24.2 - - + +
172A LEU* 3.9 16.4 - - + +
177A ARG* 1.3 74.4 - - - +
179A ILE* 1.3 66.1 + - - +
180A LEU* 4.1 20.0 - - + -
192A GLU 3.7 0.7 - - - +
193A GLN* 3.4 4.3 - - - -
194A TYR* 2.8 52.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
67A ALA* 5.6 3.1 - - - -
70A LEU* 4.3 15.5 - - + -
71A LEU* 3.8 31.2 - - + -
155A ILE 2.9 9.3 + - - +
156A HIS* 3.6 14.2 - - + -
157A VAL* 3.0 26.6 + - - +
177A ARG* 4.2 5.2 - - + -
178A LEU* 1.3 74.5 - - - +
180A LEU* 1.3 63.4 + - - +
191A LEU* 3.7 30.1 - - + -
192A GLU 3.5 1.3 - - - -
193A GLN* 3.7 42.8 - - + +
207A LEU* 4.0 9.0 - - + -
212A TYR* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.5 26.2 - - + -
161A ALA* 4.4 6.3 - - + -
164A VAL* 4.1 8.7 - - + -
165A PRO* 3.6 33.9 - - + -
168A LEU* 4.7 2.7 - - + -
178A LEU* 4.1 10.5 - - + -
179A ILE* 1.3 76.8 - - - +
181A PRO* 1.3 76.7 - - + +
182A VAL* 3.7 9.3 + - + -
191A LEU* 3.8 5.2 - - - -
192A GLU* 2.9 31.5 + - + +
194A TYR* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL 3.1 15.5 - - - +
159A ALA 3.3 16.6 - - - +
160A ALA* 3.7 16.2 - - + -
161A ALA* 2.9 23.3 + - - -
180A LEU* 1.3 89.3 - - + +
182A VAL* 1.3 63.6 + - - +
189A GLN* 4.8 1.6 - - + +
190A MET 3.5 6.5 - - - +
191A LEU* 4.2 5.6 - - + -
210A VAL* 4.2 6.3 - - + -
212A TYR* 3.4 52.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
161A ALA 3.2 10.5 - - - +
162A PRO 3.8 13.9 - - - +
163A VAL* 4.8 1.1 - - - -
164A VAL* 3.6 32.5 - - + +
180A LEU* 4.0 17.7 - - + +
181A PRO* 1.3 79.4 - - - +
183A GLY* 1.3 62.1 + - - +
188A ASN 4.3 0.7 - - - +
189A GLN* 3.4 2.5 - - - -
190A MET* 2.8 42.2 + - - +
192A GLU* 4.0 24.2 - - - +
----------------------------------------------------------
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