Contacts of the strand formed by residues 175 - 183 (chain A) in PDB entry 1P01
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 175 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PRO* 3.7 14.1 - - - +
170A ASN* 5.0 0.2 - - - -
171A TYR* 2.9 31.6 + - - +
172A ALA 3.3 1.0 + - - -
174A GLU* 1.3 77.6 - - - +
176A ALA* 1.3 66.1 + - - -
177A VAL* 3.7 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PRO* 3.7 0.3 - - - +
100A GLY* 2.8 31.2 + - - -
168A THR* 3.7 14.1 - - + -
169A ALA 3.2 8.1 - - - -
170A ASN* 3.6 20.8 + - - +
175A GLY* 1.3 72.8 - - - -
177A VAL* 1.3 54.5 + - - +
178A ARG* 3.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 4.0 4.9 - - + -
99A PRO* 3.9 9.4 - - + -
100A GLY 3.3 8.1 - - - +
101A ASN* 3.6 38.1 - - - +
102A ASP* 3.9 5.8 - - + -
167A VAL 3.9 1.4 - - - +
168A THR* 3.3 2.1 - - - -
169A ALA 2.7 33.2 + - - +
171A TYR* 3.8 31.4 - - + -
176A ALA* 1.3 75.8 - - - +
178A ARG* 1.3 64.6 + - - +
180A LEU* 3.8 30.6 - - + +
214A SER* 4.8 0.4 - - - +
229A GLU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY* 2.9 20.6 + - - +
101A ASN* 4.7 5.6 - - - +
166A ASN* 5.7 0.2 - - - +
167A VAL 4.0 2.5 - - - -
168A THR* 3.6 22.6 + - + +
170A ASN* 5.2 1.2 + - - -
176A ALA* 3.8 27.1 + - + +
177A VAL* 1.3 85.0 - - - +
179A GLY* 1.4 66.7 - - - +
180A LEU* 3.3 6.0 + - - +
229A GLU* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 3.2 33.8 + - - +
167A VAL 3.2 6.5 + - - -
168A THR* 4.8 0.6 + - - -
178A ARG* 1.4 76.5 - - - +
180A LEU* 1.3 66.0 + - - +
181A THR 4.0 0.3 + - - -
229A GLU* 4.8 4.5 - - - +
230A ARG* 4.0 22.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
165A LYS 3.6 0.2 - - - -
166A ASN 3.0 6.5 + - - -
167A VAL* 2.6 51.5 + - + +
169A ALA* 3.7 30.3 - - + -
171A TYR* 4.2 7.4 - - - +
177A VAL* 3.8 33.7 - - + +
178A ARG 4.2 0.9 - - - +
179A GLY* 1.3 75.7 - - - +
181A THR* 1.3 61.2 + - - +
214A SER* 4.2 8.5 - - - +
227A LEU* 3.9 24.5 - - + -
228A PHE 3.5 24.9 - - - +
229A GLU* 3.8 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 5.0 0.7 + - - -
162A ILE* 3.5 23.1 - - + -
164A ALA 3.4 12.3 - - - +
165A LYS* 3.8 23.1 - - + +
166A ASN 4.8 0.3 + - - -
179A GLY 4.0 0.4 + - - -
180A LEU* 1.3 73.7 - - - +
182A GLN* 1.3 64.4 + - - +
227A LEU* 3.2 6.6 - - - -
228A PHE* 2.9 70.3 + - + -
230A ARG* 3.9 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE* 3.4 6.0 - - - +
163A THR* 2.6 55.7 + - - +
164A ALA* 2.6 30.0 + - + +
167A VAL* 4.2 15.2 - - + +
180A LEU 4.2 0.4 + - - -
181A THR* 1.3 77.8 - - - +
183A GLY* 1.3 63.0 + - - +
224A ARG 4.7 4.1 + - - +
225A SER* 3.1 29.1 + - - +
226A SER 3.6 2.9 - - - +
227A LEU* 3.6 17.9 - - + +
228A PHE* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR 3.1 13.7 - - - -
162A ILE* 4.0 3.8 - - - -
163A THR* 4.1 4.0 - - - -
181A THR 4.2 0.4 + - - -
182A GLN* 1.3 77.4 - - - +
184A ASN* 1.3 62.3 + - - +
190A ALA 3.5 2.5 - - - -
199A TRP* 4.0 18.4 - - - -
224A ARG 4.1 1.9 - - - +
226A SER* 2.9 34.5 + - - -
----------------------------------------------------------
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