Contacts of the strand formed by residues 261 - 269 (chain B) in PDB entry 1R37
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 261 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS 4.6 0.7 - - - +
240B GLY* 4.5 1.1 - - - -
241B VAL 3.4 9.0 - - - +
243B ALA 4.6 0.2 - - - -
244B VAL* 3.7 26.2 - - + +
257B TYR 4.3 1.3 - - - +
258B PRO* 3.3 26.6 + - + +
259B LYS 3.3 3.7 - - - +
260B ALA* 1.3 80.0 - - - +
262B ALA* 1.3 67.9 + - - +
265B GLY 4.0 20.4 - - - +
266B LYS 4.0 11.2 - - - +
267B TYR* 4.0 25.6 - - + -
287B SER* 6.2 0.2 - - - -
289B ILE* 4.1 35.0 - - + +
290B GLN 5.0 0.2 - - - +
291B PHE* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.7 13.0 - - - +
239B LYS* 3.0 32.5 - - + +
240B GLY 3.9 8.5 - - - +
241B VAL 2.8 19.7 + - - +
242B ASP* 4.2 7.6 - - - +
260B ALA 3.7 1.2 + - - -
261B LEU* 1.3 77.7 - - - +
263B LYS* 1.3 68.8 + - - +
264B GLN 3.4 0.2 + - - -
265B GLY* 2.9 12.6 + - - -
287B SER* 5.5 1.1 - - - -
289B ILE* 3.7 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 2.8 41.1 + - + +
111A LEU* 2.7 47.0 + - + +
112A CYS 3.5 11.3 + - - -
113A ASP* 3.2 22.8 + - - +
239B LYS 4.8 0.2 + - - -
242B ASP* 4.8 3.5 - - - +
262B ALA* 1.3 78.2 - - - +
264B GLN* 1.3 67.1 + - - +
265B GLY* 3.2 2.6 + - - -
286B LEU 5.3 1.8 - - - +
287B SER* 3.4 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 5.4 0.5 - - - -
103A TYR* 3.8 13.9 - - + -
106A ILE* 3.8 9.5 - - - +
108A GLU* 3.4 38.6 + - - +
111A LEU* 3.3 25.4 - - + -
161A ARG* 3.7 4.4 - - - +
165A LYS* 5.1 3.4 - - - +
172B LYS* 5.7 0.6 + - - +
242B ASP* 4.3 1.9 - - - +
263B LYS* 1.3 72.1 - - - +
265B GLY* 1.3 66.1 + - - +
266B LYS* 3.4 24.8 + - - +
287B SER 2.8 13.7 + - - -
288B GLU* 3.4 31.4 + - + +
290B GLN* 4.9 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL 4.3 1.8 - - - -
242B ASP* 3.3 18.4 - - - -
261B LEU* 4.0 12.9 - - - +
262B ALA 2.9 17.9 + - - -
263B LYS 3.1 1.6 + - - -
264B GLN* 1.3 79.8 - - - +
266B LYS* 1.3 59.8 + - - +
289B ILE* 3.3 8.9 - - - +
290B GLN 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS 3.5 21.1 - - - +
166B ALA* 4.0 16.8 - - - +
167B SER* 3.4 18.8 - - - +
172B LYS* 4.2 18.0 - - - +
242B ASP 3.0 11.3 + - - +
243B ALA* 3.2 3.1 - - - +
244B VAL 2.8 27.9 + - - +
261B LEU* 4.0 2.2 - - - +
264B GLN* 3.4 18.7 + - - +
265B GLY* 1.3 74.3 - - - +
267B TYR* 1.3 60.7 + - - +
268B VAL* 3.6 5.3 + - + +
290B GLN* 3.7 37.8 - - + +
292B VAL* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 3.6 26.8 - - + +
246B ASP* 2.6 43.8 + - + +
249B ASN* 4.0 2.7 - - - -
253B THR 3.7 7.6 + - - -
254B LEU* 3.8 15.4 - - + +
257B TYR* 3.5 18.9 - - + +
258B PRO* 3.5 39.9 - - + +
261B LEU* 4.0 11.7 - - + -
265B GLY 4.1 0.6 + - - -
266B LYS* 1.3 70.0 - - - +
268B VAL* 1.3 64.6 + - - +
269B MET* 3.4 15.3 + - + +
290B GLN 2.8 16.7 + - - +
291B PHE* 3.5 21.6 - + + -
292B VAL* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA* 3.9 34.8 - - + +
165B LYS* 4.5 2.5 - - + +
166B ALA* 4.1 23.3 - - + +
244B VAL 2.7 18.3 + - - +
245B ILE* 3.5 7.7 - - + -
246B ASP* 3.0 27.5 + - - +
266B LYS* 4.2 7.2 - - + +
267B TYR* 1.3 69.9 - - - +
269B MET* 1.3 61.8 + - - +
270B VAL* 3.6 4.1 + - + +
292B VAL* 3.3 21.1 - - + +
294B SER* 3.9 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA* 3.6 30.5 - - + +
284A ILE* 4.0 30.7 - - + -
285A THR* 3.0 19.1 + - - +
249B ASN* 3.3 33.7 - - - +
254B LEU* 4.2 9.9 - - + -
267B TYR* 3.6 20.4 - - + +
268B VAL* 1.3 69.8 - - - +
270B VAL* 1.3 60.3 + - - +
277B LEU* 4.3 5.2 - - + -
291B PHE* 4.1 27.8 - - - -
292B VAL 2.8 14.0 + - - +
293B GLY* 3.7 3.5 - - - -
294B SER 3.4 17.4 + - - -
----------------------------------------------------------
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