Contacts of the strand formed by residues 68 - 74 (chain B) in PDB entry 3OTC
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 ILE 68 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.9 35.7 - - + +
62B MET* 3.7 36.5 + - + +
65B LEU* 4.2 6.7 - - + -
66B GLU* 3.3 3.3 - - - +
67B ASP* 1.3 77.5 - - - +
69B VAL* 1.3 60.6 + - - +
70B ILE 4.1 11.2 - - - +
80B PHE* 4.2 11.2 - - + -
81B VAL 3.4 14.1 - - - +
82B PHE* 3.5 39.3 - - + -
83B LYS* 5.9 0.2 - - - -
214B TRP* 2.8 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 4.1 20.9 - - + -
62B MET* 4.5 2.7 - - - -
67B ASP 3.7 0.2 + - - -
68B ILE* 1.3 75.6 - - - +
70B ILE* 1.3 63.9 + - + +
81B VAL* 2.9 19.4 + - + +
83B LYS* 3.6 38.8 - - + +
212B LEU 4.1 5.0 - - - +
213B ILE* 4.1 9.7 - - - +
214B TRP* 4.1 15.5 + - + -
263B GLU 5.8 0.7 - - - +
264B ILE* 3.9 36.9 - - + +
267B GLU* 5.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B MET* 4.7 0.9 - - - -
68B ILE* 3.8 4.1 - - - +
69B VAL* 1.3 85.9 - - + +
71B ALA* 1.3 67.3 + - - +
72B TYR* 5.7 0.2 - - + -
81B VAL* 3.0 52.9 + - + +
140B LEU* 5.5 2.2 - - + -
144B LEU* 4.5 18.8 - - + -
211B VAL* 4.0 23.8 - - + -
212B LEU 3.4 11.4 - - - +
213B ILE* 4.2 5.6 - - + -
252B ILE* 5.4 3.6 - - + -
257B PHE* 4.0 20.4 - - + -
258B TRP* 4.0 18.2 - - + -
264B ILE* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B MET* 3.7 26.5 - - - -
68B ILE* 4.8 0.4 - - + -
70B ILE* 1.3 82.3 - - - +
72B TYR* 1.3 60.0 + - - +
78B TYR* 4.2 3.7 - - + -
79B SER 3.1 14.1 - - - +
80B PHE* 4.0 16.8 - - + -
81B VAL* 5.7 0.7 - - - -
210B THR 3.9 0.7 - - - +
211B VAL* 3.6 2.3 - - - -
212B LEU* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 5.7 0.7 - - + -
71B ALA* 1.3 75.6 - - - +
73B GLY* 1.3 56.9 + - - +
74B GLN* 4.1 15.5 - - + -
77B GLU* 5.0 2.4 - - - +
78B TYR* 3.4 3.5 - - - -
79B SER* 2.6 41.0 + - - -
81B VAL* 6.3 0.2 - - - +
144B LEU* 4.0 24.7 - - + +
147B ARG* 3.7 40.8 - - + -
148B GLN* 3.2 29.1 - - + +
151B CYS* 3.5 11.4 - - - +
208B LYS 2.6 30.6 + - - -
209B GLY* 3.7 4.4 - - - -
210B THR 2.9 28.9 - - - -
211B VAL* 3.6 17.3 - - + -
252B ILE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 5.9 1.0 - - - +
72B TYR* 1.3 79.3 - - - +
74B GLN* 1.3 61.8 + - - +
77B GLU* 3.2 15.5 - - - -
78B TYR* 3.4 24.1 - - - -
209B GLY* 4.0 0.7 - - - -
210B THR* 3.2 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.8 2.7 - - - -
72B TYR* 4.0 8.3 - - + +
73B GLY* 1.3 75.0 - - - +
75B SER* 1.3 84.7 + - - +
77B GLU* 2.8 54.8 + - - +
147B ARG* 3.9 14.7 + - - +
150B ASP* 3.1 24.8 + - - +
151B CYS* 3.6 42.9 - - + +
154B ASN* 4.8 6.3 + - - +
209B GLY* 4.8 2.7 - - - -
----------------------------------------------------------
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