Contacts of the helix formed by residues 300 - 313 (chain A) in PDB entry 1OH7
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 THR 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 5.5 3.1 - - - -
298A THR* 3.8 4.6 + - - -
299A VAL* 1.3 81.3 - - + +
301A PRO* 1.3 70.5 - - - +
302A MET* 3.3 16.8 - - + +
303A GLY* 3.1 22.9 + - - -
304A SER* 3.1 9.8 + - - -
342A LEU* 3.0 33.4 - - + +
343A ARG* 4.3 0.2 - - - -
345A VAL* 4.7 0.2 - - + -
346A GLY* 3.5 27.4 - - - +
549A LEU 5.6 0.4 - - - +
553A ASP* 3.0 17.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 3.5 47.4 - - + +
128A ARG* 4.8 7.2 - - + +
299A VAL 4.7 0.7 - - - +
300A THR* 1.3 86.0 - - - +
302A MET* 1.3 63.5 + - - +
304A SER* 3.1 10.4 + - - +
305A ARG* 3.0 27.2 + - - +
346A GLY* 4.0 3.6 - - - -
347A ASP* 3.6 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A THR* 3.3 14.6 - - + +
301A PRO* 1.3 79.6 - - - +
303A GLY* 1.3 59.6 + - - +
305A ARG* 3.3 26.3 + - - +
306A MET* 3.1 28.6 + - - +
309A ARG* 5.0 1.6 + - - -
345A VAL* 3.9 13.0 - - + -
346A GLY 3.4 18.6 - - - +
347A ASP* 3.9 2.4 + - - +
348A LEU* 4.0 7.0 - - + +
349A GLU* 3.9 36.5 - - - +
546A ALA 3.6 17.3 - - - +
549A LEU* 3.8 29.6 - - + -
550A ALA* 3.7 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 3.6 7.9 - - - +
300A THR* 3.1 12.2 + - - -
302A MET* 1.3 79.2 - - - +
304A SER* 1.3 59.5 + - - +
307A LEU* 3.2 9.5 + - - +
550A ALA* 3.8 20.9 - - - -
553A ASP* 3.4 17.7 - - - -
554A VAL* 3.2 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 3.5 39.7 + - - +
296A ASP* 3.4 21.0 + - - +
298A THR* 3.1 21.6 + - - -
300A THR 3.1 6.6 + - - -
301A PRO 3.1 8.4 + - - -
303A GLY* 1.3 75.3 - - - +
305A ARG* 1.3 65.0 + - - +
307A LEU* 3.5 2.3 + - - +
308A LYS* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU 3.3 17.4 + - - -
128A ARG 3.7 3.8 - - - +
129A GLN 3.6 24.5 - - - +
130A ASP* 3.5 27.2 + - - +
149A ASP* 5.0 2.2 + - - -
151A SER* 5.0 1.6 + - - -
154A ARG* 4.9 0.4 - - - +
301A PRO 3.0 14.4 + - - +
302A MET* 3.3 22.7 - - - +
304A SER* 1.3 75.7 - - - +
306A MET* 1.3 64.1 + - - +
308A LYS* 3.1 9.0 + - - +
309A ARG* 3.0 32.5 + - - +
347A ASP* 2.7 38.6 + - - -
349A GLU* 2.8 26.1 + - - +
350A ARG* 3.1 38.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET 3.1 17.0 + - - +
303A GLY* 4.4 0.4 - - - -
305A ARG* 1.3 73.0 - - - +
307A LEU* 1.3 64.0 + - - +
309A ARG* 3.2 32.2 + - - +
310A TRP* 3.0 59.0 + - + +
349A GLU* 5.7 3.4 - - - +
547A SER* 4.5 16.8 - - - +
550A ALA* 3.9 12.1 - - + -
551A GLU* 3.6 38.8 - - + +
554A VAL* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.2 2.2 - - + +
296A ASP* 3.5 41.7 - - + +
298A THR* 3.7 9.2 - - + -
303A GLY 3.2 15.6 + - - +
304A SER 3.6 4.3 - - - +
306A MET* 1.3 78.1 - - - +
308A LYS* 1.3 59.7 + - + +
310A TRP* 3.2 5.2 + - + +
311A LEU* 2.9 57.3 + - + +
554A VAL* 3.8 24.8 - - + +
557A ASN* 3.7 14.8 - - - +
558A LEU* 4.2 20.4 - - + -
636A ILE* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 3.1 34.0 + - - +
129A GLN* 4.3 18.1 - - + +
130A ASP* 5.7 1.1 - - - +
280A THR* 3.9 26.5 - - + +
292A ALA* 4.7 14.5 - - + +
296A ASP* 3.6 23.0 + - - +
304A SER* 3.2 13.3 + - - +
305A ARG* 3.1 10.6 + - - +
307A LEU* 1.3 81.5 - - + +
309A ARG* 1.3 59.9 + - + +
311A LEU* 3.9 8.0 - - + +
312A HIS* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP* 3.1 30.2 + - - +
154A ARG* 3.5 49.3 - - - +
172A ARG* 5.3 4.3 + - - +
302A MET 5.0 1.2 + - - -
305A ARG* 3.0 21.1 + - - +
306A MET* 3.2 49.8 + - - +
308A LYS* 1.3 75.9 - - + +
310A TRP* 1.3 65.5 + - + +
312A HIS* 3.4 5.8 + - - +
313A MET* 2.8 33.7 + - + +
349A GLU* 5.2 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A MET* 3.0 48.8 + - + +
307A LEU* 3.7 5.4 - - + +
309A ARG* 1.3 76.9 - - + +
311A LEU* 1.3 69.0 + - - +
313A MET* 2.7 29.6 + - - +
315A VAL* 6.3 0.4 - - + -
324A ARG* 3.4 53.1 - - + +
551A GLU* 4.0 27.1 - - + -
554A VAL* 3.5 30.3 - - + -
555A LEU* 3.8 20.4 - - + -
558A LEU* 4.6 3.4 - - + -
636A ILE* 3.4 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A MET* 4.2 3.5 - - - +
279A ILE* 3.8 17.6 - - + +
280A THR* 5.2 0.4 - - + -
291A LEU* 3.8 18.6 - - + -
292A ALA* 4.5 23.3 - - + -
295A LEU* 3.9 21.8 - - + -
307A LEU* 2.9 49.4 + - + +
308A LYS* 3.9 10.3 - - + +
310A TRP* 1.3 71.9 - - - +
312A HIS* 1.3 59.3 + - - +
314A PRO* 4.3 1.0 - - - +
632A LEU* 3.5 30.5 - - + +
633A MET* 5.7 0.4 - - + -
636A ILE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLN 5.6 1.4 + - - -
172A ARG* 3.7 26.6 + - + +
267A ILE 5.1 0.2 - - - +
269A MET* 4.6 2.5 - - - +
274A ARG* 3.1 65.9 + - + +
279A ILE* 3.6 20.0 - - + +
280A THR* 2.9 39.0 + - + +
308A LYS* 3.0 24.5 + - - +
309A ARG* 3.7 6.3 - - - +
310A TRP 2.8 2.0 + - - -
311A LEU* 1.3 77.7 - - - +
313A MET* 1.3 59.8 + - + +
314A PRO* 3.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 5.4 0.9 - - - +
172A ARG* 3.5 35.4 - - - +
261A GLU* 3.2 42.0 - - + +
266A SER* 3.9 24.2 - - - -
267A ILE 5.1 1.1 - - - +
309A ARG* 2.8 13.9 + - + +
310A TRP* 2.7 21.8 + - - +
312A HIS* 1.3 74.5 - - - +
314A PRO* 1.3 63.7 - - - +
315A VAL* 3.5 10.3 + - + +
----------------------------------------------------------
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