Contacts of the strand formed by residues 196 - 205 (chain A) in PDB entry 1BY7
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 MET 196 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.9 0.9 - - + -
129A LEU* 3.7 25.4 - - + -
130A PHE 3.3 15.3 - - - +
131A GLY* 4.5 1.1 - - - -
137A PHE* 4.2 5.6 - - - -
158A PHE* 4.3 0.9 - - - -
194A THR* 3.9 1.6 - - - +
195A ARG* 1.3 83.4 - - - +
197A VAL* 1.3 65.5 + - - +
340A PHE* 4.0 16.8 - - + -
343A MET* 3.3 39.9 - - + +
349A LEU* 3.8 14.6 - - + -
350A PHE 3.2 27.3 + - - +
351A LEU* 3.7 16.3 - - + +
352A SER* 2.8 33.8 + - - -
353A GLU 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS 4.0 0.9 - - - +
129A LEU* 3.7 6.0 - - - -
130A PHE* 3.0 40.0 + - + +
158A PHE* 4.2 2.0 - - + -
169A ILE* 3.8 28.3 - - + -
190A VAL* 3.9 13.2 - - + -
194A THR* 3.7 24.2 - - + -
196A MET* 1.3 80.4 - - - +
198A LEU* 1.3 59.7 + - - +
199A VAL* 4.7 6.1 - - + -
351A LEU* 4.4 0.9 - - - -
352A SER* 4.1 7.2 - - - -
353A GLU* 3.4 11.9 - - + +
355A PHE* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 3.7 40.8 - - + +
39A MET* 3.9 25.8 - - - -
41A MET* 4.7 9.4 - - + -
42A VAL* 4.2 6.7 - - + -
127A ASN* 5.0 0.7 - - + -
128A LYS 3.6 22.4 - - - +
129A LEU* 4.2 18.4 - - + +
197A VAL* 1.3 74.4 - - - +
199A VAL* 1.3 68.7 + - - +
200A ASN* 5.2 1.1 - - + -
351A LEU* 4.4 4.6 - - + +
353A GLU 3.1 9.6 + - - +
354A VAL* 3.3 16.0 - - + -
355A PHE* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL 5.4 0.4 - - - +
127A ASN* 3.3 5.6 - - - +
128A LYS 2.9 45.7 + - - +
130A PHE* 3.9 13.2 - - + -
169A ILE* 3.8 24.2 - - + -
172A TRP* 3.9 21.5 - - + -
173A VAL* 4.2 7.0 - - + -
184A LEU* 3.6 22.4 - - + -
185A LEU* 3.9 9.0 - - + -
197A VAL* 4.7 2.9 - - + -
198A LEU* 1.3 82.7 - - - +
200A ASN* 1.3 63.5 + - - +
355A PHE* 3.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 2.6 38.0 + - - -
35A ILE* 3.9 2.0 - - - +
38A THR* 4.2 17.7 + - + +
125A SER* 3.6 17.2 + - - -
126A VAL 3.3 12.4 - - - +
127A ASN* 4.1 4.7 - - - +
184A LEU* 4.8 2.6 - - - +
198A LEU* 5.2 2.9 - - + -
199A VAL* 1.3 77.7 - - - +
201A ALA* 1.3 62.5 + - - +
202A VAL* 3.6 2.1 - - - +
354A VAL* 5.9 3.1 - - + -
355A PHE 2.9 11.9 + - - +
356A HIS* 2.9 26.7 + - + +
357A GLN* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU 4.7 0.2 - - - -
125A SER* 3.6 0.3 - - - -
126A VAL* 3.0 46.1 + - + +
173A VAL* 5.2 6.1 - - + -
177A THR* 4.2 16.6 - - + -
181A ILE* 4.8 8.5 - - + -
184A LEU* 5.3 4.3 - - + -
200A ASN* 1.3 74.2 + - - +
202A VAL* 1.3 64.3 - - - +
357A GLN* 3.1 16.6 - - + +
359A MET* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 4.3 5.4 - - - +
33A TRP* 4.4 10.5 - - + -
34A SER* 3.3 26.9 - - - +
123A LEU* 4.6 1.6 - - + -
124A GLU 3.1 22.2 - - - +
125A SER* 3.3 17.7 - - - +
200A ASN* 3.6 7.4 - - - +
201A ALA* 1.3 81.7 - - - +
203A TYR* 1.3 62.7 + - - +
356A HIS* 4.4 2.2 - - + -
357A GLN 2.7 9.6 + - - +
358A ALA* 3.5 2.2 - - - -
359A MET* 3.0 28.8 + - - +
408A PHE* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.6 18.4 - - + +
123A LEU* 3.5 5.9 - - - +
124A GLU* 2.6 53.9 + - + +
180A LYS* 3.7 32.5 - - + +
202A VAL* 1.3 75.6 - - - +
204A PHE* 1.3 67.7 + - - +
205A LYS* 3.1 37.0 - - + -
359A MET* 3.4 39.9 - - + -
361A ASP* 2.2 42.5 + - - -
408A PHE* 4.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU 3.1 19.5 - - - -
123A LEU* 3.9 22.0 - - + -
203A TYR* 1.3 81.5 - - - +
205A LYS* 1.3 61.2 + - - +
206A GLY* 3.5 27.6 - - - -
258A TYR* 3.5 26.9 - + + -
262A VAL* 3.9 32.1 - - + -
359A MET 3.0 9.0 + - - +
360A VAL* 3.2 32.9 - - + +
361A ASP 3.2 5.0 + - - -
398A ILE* 3.6 20.2 - - + -
407A LEU* 5.4 2.2 - - + -
408A PHE* 3.5 24.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 2.8 49.4 + - + +
203A TYR* 3.1 35.4 - - + +
204A PHE* 1.3 79.1 - - - +
206A GLY* 1.3 68.7 + - - +
313A LYS* 6.1 0.8 - - - +
361A ASP* 3.5 31.8 + - + +
363A ASN* 4.2 15.9 - - - +
365A GLU* 4.1 18.8 + - - +
----------------------------------------------------------
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