Contacts of the strand formed by residues 315 - 322 (chain A) in PDB entry 2OHF
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 GLU 315 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 3.6 1.5 - - - +
82A SER* 2.5 34.5 + - - +
84A ILE* 3.6 10.6 - - + +
310A THR* 3.3 9.0 + - - +
311A ALA 3.7 0.2 - - - -
312A GLY* 2.9 25.7 + - - -
314A ASP* 1.3 87.0 - - + +
316A VAL* 1.3 75.7 + - - +
317A ARG* 3.9 31.1 + - + +
319A TRP* 4.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.0 19.1 - - + +
74A LEU* 3.8 45.3 - - + +
75A CYS* 4.2 9.2 - - - +
78A HIS* 4.3 2.5 - - + +
80A PRO* 3.7 21.0 - - + +
82A SER 3.0 9.7 + - - +
83A LYS* 3.5 0.7 - - - -
84A ILE 3.0 23.4 + - - -
309A PHE* 4.9 2.9 - - + -
310A THR 3.2 4.5 - - - +
311A ALA* 3.9 18.8 - - + -
312A GLY 4.2 3.6 - - - +
315A GLU* 1.3 78.5 - - - +
317A ARG* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.2 1.6 - - - -
84A ILE* 3.1 42.4 - - + +
308A PHE 3.4 0.2 - - - +
309A PHE* 3.2 12.4 - - - -
310A THR* 3.1 40.1 + - - +
315A GLU* 3.9 19.8 + - + -
316A VAL* 1.3 77.7 - - - +
318A ALA* 1.3 75.1 + - - +
319A TRP* 3.5 48.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.0 3.1 - - + -
84A ILE 2.8 8.5 + - - +
85A PRO* 3.6 10.2 - - + +
86A ALA* 3.2 29.5 + - - +
307A TYR* 3.8 27.1 - - + -
308A PHE 3.3 5.2 - - - -
309A PHE* 4.3 8.1 - - + -
317A ARG* 1.3 87.8 + - - +
319A TRP* 1.3 59.3 - - - +
320A THR* 4.0 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 3.1 3.4 - - - +
308A PHE* 2.7 74.4 + + + -
310A THR* 3.0 28.9 + - + +
315A GLU* 4.8 4.3 - - - -
317A ARG* 3.5 61.8 - - - +
318A ALA* 1.3 72.5 - - - +
320A THR* 1.3 64.2 + - - +
321A ILE 3.5 0.2 + - - -
333A LYS* 3.2 43.1 - - + -
334A ILE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.8 20.5 + - - +
86A ALA* 3.7 14.0 - - - +
87A PHE 4.8 2.4 + - - -
300A PHE* 3.6 26.1 - - + -
305A LEU* 3.4 33.4 - - + -
306A GLU 3.2 11.0 - - - +
307A TYR* 3.9 2.9 - - - +
318A ALA 4.0 1.4 + - - -
319A TRP* 1.3 71.0 - - - +
321A ILE* 1.3 69.4 + - - +
333A LYS* 3.8 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 4.2 5.8 - - - -
305A LEU* 3.4 7.9 - - - -
306A GLU* 2.5 65.3 + - + +
307A TYR* 4.2 4.5 - - - -
308A PHE* 3.9 25.6 - - + -
319A TRP 4.0 4.7 - - - +
320A THR* 1.3 81.4 - - - +
322A ARG* 1.3 71.1 + - - +
324A GLY 5.8 0.2 - - - +
325A THR* 3.9 22.2 - - + +
330A ALA* 4.6 1.8 - - - -
333A LYS* 4.2 16.8 - - + -
377A VAL* 4.1 34.3 - - + +
378A GLU 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE 4.1 13.5 + - - -
17A GLY* 5.6 0.2 - - - -
18A ARG 2.9 27.5 + - - -
19A PHE* 5.0 1.2 - - - +
20A GLY* 2.7 57.4 + - - +
21A THR* 4.4 5.3 - - + +
23A LEU* 4.0 14.9 - - - +
303A LEU 5.0 1.8 - - - -
304A GLN* 3.7 24.7 + - - +
305A LEU* 3.8 12.6 - - - -
306A GLU* 4.5 1.8 - - - -
321A ILE* 1.3 77.7 - - - +
323A LYS* 1.3 72.6 + - - +
324A GLY 3.2 0.2 + - - -
325A THR* 2.8 30.8 + - - +
----------------------------------------------------------
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