Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 1SID
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 GLN 161 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 3.3 15.5 + - - +
160A SER* 1.3 75.9 - - - +
162A TYR* 1.3 65.4 + - - +
163A HIS* 4.2 8.4 + - + +
243A TYR* 3.8 3.9 - - - -
244A THR* 2.8 54.8 + - - +
249A THR* 3.6 4.2 + - - +
250A PRO 2.8 29.3 + - - -
251A PRO* 3.0 29.0 - - - +
252A VAL* 3.2 17.1 + - - +
285A ILE* 3.2 18.6 - - - +
286A MET* 3.6 15.5 + - - +
136E LEU* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 4.4 8.3 - - - -
161A GLN* 1.3 76.3 - - - +
163A HIS* 1.3 65.1 + - - +
164A VAL* 3.2 24.0 - - + +
224A VAL* 3.6 22.3 + - + +
227A TRP 4.6 3.1 + - - -
228A HIS* 4.3 6.1 + - - -
229A PRO* 4.9 2.4 - - - +
242A ASN 3.3 17.5 - - - -
243A TYR* 4.1 14.4 - + + -
283A VAL* 3.0 19.4 - - + +
285A ILE* 2.7 53.6 + - + +
133E GLY* 3.6 24.3 - - - -
136E LEU* 3.9 21.5 - - + -
255E PHE* 3.2 32.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 5.1 2.8 - - + +
161A GLN* 4.2 9.5 + - + +
162A TYR* 1.3 82.6 + - - +
164A VAL* 1.3 60.0 + - - +
241A GLY* 2.9 3.8 - - - -
242A ASN* 2.8 45.6 + - - +
244A THR* 5.7 1.6 - - - -
252A VAL 5.0 2.2 + - - -
253A LEU* 4.0 16.1 - - + +
283A VAL 2.9 7.9 - - - -
284A ASP* 3.0 37.4 + - + +
285A ILE 3.1 23.6 + - - -
286A MET* 3.3 31.0 - - + +
304A ARG* 4.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 4.0 15.0 - - + -
162A TYR* 3.2 42.8 - - + +
163A HIS* 1.3 82.7 - - - +
165A PHE* 1.3 79.0 + - - +
229A PRO* 5.2 3.8 - - + -
239A TYR* 5.0 6.5 - - + -
240A PHE* 3.0 27.8 - - - +
241A GLY* 3.5 1.1 - - - +
282A CYS* 3.0 2.2 - - - +
283A VAL* 2.8 33.2 + - + -
284A ASP* 4.0 0.6 + - - -
304A ARG* 3.9 3.3 + - - +
255E PHE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 4.8 4.0 - - - -
125A VAL* 5.0 6.5 - - + -
127A THR* 3.9 24.2 - - + -
164A VAL* 1.3 81.8 - - - +
166A ALA* 1.3 82.5 + - - +
167A VAL* 4.3 11.7 - - + -
239A TYR* 2.9 3.1 - - - +
240A PHE* 2.6 85.8 + + + +
241A GLY* 5.6 0.2 - - - -
261A THR* 5.9 3.6 - - + -
281A SER 2.9 18.2 - - - +
282A CYS* 3.3 11.0 - - + +
304A ARG* 3.6 30.1 - - - +
306A PHE* 4.3 11.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 6.4 0.4 - - + -
165A PHE* 1.3 87.1 - - - +
167A VAL* 1.3 67.1 + - - +
172A LEU* 5.1 7.6 - - + -
237A THR* 3.5 13.2 - - + -
238A ARG 2.7 21.8 - - - +
239A TYR* 3.2 14.6 - - + -
280A LEU* 3.5 2.9 - - - +
281A SER* 2.9 35.1 + - - +
306A PHE* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA* 5.0 4.7 - - + -
125A VAL* 4.6 7.9 - - + -
165A PHE* 4.3 16.2 - - + -
166A ALA* 1.3 86.8 - - - +
168A GLY* 1.3 59.9 + - - +
237A THR* 3.1 12.6 - - - +
238A ARG* 2.9 17.0 + - + +
240A PHE* 5.5 0.9 - - + -
263A LEU* 4.4 31.6 - - + -
271A PRO* 3.6 8.6 - - + +
278A LEU* 3.7 10.5 - - + -
279A TYR 3.3 3.4 - - - -
280A LEU* 3.6 23.6 - - + -
306A PHE* 5.0 7.0 - - + -
308A ILE* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 1.3 77.9 - - - +
169A GLY* 1.3 56.7 + - - -
170A GLU 3.2 9.9 - - - -
236A ASN 3.3 10.3 - - - -
237A THR* 3.4 12.7 - - - +
271A PRO* 4.2 6.1 - - - -
273A CYS* 5.4 0.7 - - - -
278A LEU* 3.7 8.0 - - - +
279A TYR* 2.8 44.5 + - - -
----------------------------------------------------------
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