Contacts of the strand formed by residues 36 - 43 (chain B) in PDB entry 1OGS
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 36 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PRO* 3.3 12.0 - - - +
33B ALA* 2.6 42.3 + - + +
34B LEU 4.4 3.8 - - - +
35B GLY* 1.3 85.8 + - - +
37B PHE* 1.3 61.5 + - - +
53B MET* 4.0 22.5 - - + +
54B GLY 3.2 13.7 - - - +
55B PRO* 4.7 4.0 - - + -
56B ILE* 3.6 12.7 - - - +
494B TRP* 3.7 8.3 - - - +
495B HIS 4.7 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PRO* 4.2 4.3 - - - -
36B THR* 1.3 76.2 - - - +
38B SER* 1.3 71.4 + - - +
39B ARG* 3.7 40.6 - - + -
53B MET* 3.3 8.1 - - - +
54B GLY* 2.8 61.8 + - - -
55B PRO* 3.5 18.8 - - + -
56B ILE* 4.2 2.0 - - + -
480B LEU* 3.6 35.9 - - + -
481B GLU 4.6 12.6 - - - -
482B THR* 5.2 1.3 - - - -
492B TYR* 3.9 17.7 - + - -
493B LEU 3.4 11.4 - - - +
494B TRP* 4.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR 4.9 3.5 + - - -
32B PRO* 3.1 29.6 - - - +
37B PHE* 1.3 77.6 - - - +
39B ARG* 1.3 61.6 + - - +
40B TYR* 4.6 2.0 - - - -
51B LEU* 4.2 16.8 - - - +
52B SER 3.7 4.5 - - - -
53B MET* 4.6 3.1 - - - +
491B THR 4.4 0.7 - - - -
492B TYR* 3.3 4.9 - - - -
493B LEU* 2.8 51.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.7 25.0 - - + -
38B SER* 1.3 77.0 - - - +
40B TYR* 1.3 68.8 + - - +
41B GLU* 4.5 9.9 - - - -
50B GLU 3.2 3.6 - - - +
51B LEU* 3.4 2.4 - - - -
52B SER* 2.8 69.6 + - - +
53B MET 4.9 3.8 + - - +
54B GLY* 5.8 0.2 - - - -
481B GLU 4.6 1.4 + - - -
482B THR* 2.9 29.9 + - - +
483B ILE 5.0 0.2 - - - +
490B HIS* 3.9 22.9 + - + +
491B THR 3.5 4.0 - - - +
492B TYR* 3.4 31.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.1 21.8 - + - -
29B PRO* 5.6 3.6 - - - +
30B THR 5.1 9.0 + - - -
38B SER* 4.6 3.1 - - - -
39B ARG* 1.3 76.2 - - - +
41B GLU* 1.3 59.3 + - - +
49B MET* 3.6 21.8 - - + -
50B GLU 3.1 6.7 - - - -
51B LEU* 3.6 38.8 - - + +
422B HIS* 3.3 11.9 - - + -
425B LYS* 4.8 3.9 - - - -
426B PHE* 3.3 50.2 - + + -
490B HIS* 3.2 7.8 - - - +
491B THR* 3.0 32.5 + - - +
493B LEU* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 4.5 10.4 - - - -
40B TYR* 1.3 75.1 - - - +
42B SER* 1.3 65.3 + - - +
43B THR* 3.8 14.0 - - + +
47B ARG* 3.0 33.8 + - - +
48B ARG 3.6 4.3 + - - -
49B MET 2.9 4.7 + - - -
50B GLU* 2.8 42.2 + - + +
422B HIS* 4.1 0.2 - - - -
485B PRO* 3.6 16.6 - - - +
489B ILE 3.7 2.5 - - - -
490B HIS* 2.6 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 1.3 70.2 - - - +
43B THR* 1.3 64.2 + - - +
47B ARG 3.0 8.7 - - - -
48B ARG* 3.6 2.8 - - - -
49B MET* 2.7 27.9 + - - +
357B TRP* 3.6 11.4 - - - -
418B TYR* 4.1 8.5 - - - +
419B HIS* 5.6 0.2 - - - -
422B HIS* 2.7 24.8 + - - -
488B SER* 3.3 3.1 - - - -
489B ILE* 2.9 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 3.8 26.7 - - + +
42B SER* 1.3 80.6 - - - +
44B ARG* 1.3 64.1 + - - +
45B SER* 2.6 28.7 + - - +
46B GLY 3.1 4.7 + - - -
47B ARG* 2.9 27.1 + - - +
48B ARG* 2.8 22.5 + - - -
357B TRP* 3.3 8.3 - - - -
485B PRO* 5.0 6.1 - - + -
486B GLY 5.4 1.1 - - - -
487B TYR 3.6 7.4 - - - -
488B SER* 3.9 12.8 - - - -
----------------------------------------------------------
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