Contacts of the strand formed by residues 99 - 105 (chain B) in PDB entry 1O94
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 99 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.3 2.2 - - + -
18B LYS* 3.9 30.5 - - + +
19B THR 3.8 25.6 - - - +
20B LEU* 4.0 18.8 - - + -
54B ALA 2.9 15.8 + - - +
55B ALA* 3.2 2.8 - - + -
56B LEU 2.8 30.7 + - - -
93B VAL* 3.5 8.6 - - - +
94B HIS* 5.7 0.7 - - + +
97B GLY 5.7 0.7 - - - +
98B ALA* 1.3 77.9 - - - +
100B ALA* 1.3 56.8 + - - +
164B ASP* 3.5 26.0 - - + +
165B ILE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 3.3 6.7 - - - +
89B MET* 4.3 5.6 - - - -
90B THR* 3.9 39.5 - - + -
93B VAL* 4.2 9.6 - - + -
94B HIS* 4.4 0.9 - - - +
99B LEU* 1.3 76.0 - - - +
101B GLY* 1.3 58.8 + - - +
163B PHE* 3.7 5.5 - - + -
164B ASP* 2.8 40.5 + - - +
165B ILE* 3.2 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 3.0 9.3 + - - +
57B ASN* 3.1 22.2 - - - -
58B THR 3.0 23.0 + - - -
89B MET* 4.5 0.2 - - - +
100B ALA* 1.3 74.6 - - - +
102B VAL* 1.3 57.0 + - - -
163B PHE* 3.2 13.5 - - - -
165B ILE* 3.2 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASN* 3.7 0.8 + - - -
58B THR* 3.5 9.9 - - + +
61B CYS* 3.5 33.7 - - + -
77B ILE* 5.1 0.4 - - + -
86B LEU* 5.0 0.9 - - + -
101B GLY* 1.3 73.8 - - - -
103B GLU* 1.4 62.6 + - - +
104B LEU* 3.8 12.1 + - + -
158B SER* 3.4 33.0 - - - +
163B PHE* 3.6 30.7 - - + -
165B ILE 3.1 8.9 + - - +
166B VAL* 4.2 6.1 - - + -
167B TYR* 3.1 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 3.3 32.8 - - + +
58B THR* 3.5 5.0 + - - +
59B GLU 3.9 7.0 - - - +
60B TYR* 3.2 16.6 + - - +
61B CYS* 2.9 27.5 + - - +
102B VAL* 1.4 74.9 - - - +
104B LEU* 1.3 62.7 + - - +
105B TRP 3.2 0.2 + - - -
167B TYR* 3.8 11.2 - - + -
169B TYR* 3.1 36.3 - - + -
222B ARG* 3.7 5.9 - - - +
1730B FMN 2.6 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B CYS 3.6 2.5 - - - +
63B ILE* 3.8 9.0 - - + -
77B ILE* 4.2 7.9 - - + -
102B VAL* 4.2 15.5 - - + -
103B GLU* 1.3 68.8 - - - +
105B TRP* 1.3 60.3 + - - +
151B TYR* 3.7 44.8 - - + +
154B ALA* 4.0 15.5 - - + -
155B ALA* 3.8 8.5 - - + +
158B SER* 3.5 23.1 - - - +
166B VAL* 3.6 24.2 - - + -
167B TYR 3.1 21.6 + - - +
168B VAL* 5.5 0.2 - - + -
169B TYR* 3.3 24.8 + - - +
209B VAL* 4.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 3.5 26.7 - + + -
61B CYS 2.8 25.2 + - - +
62B SER* 3.5 21.6 - - - -
63B ILE* 3.2 27.8 + - - +
67B SER* 3.3 35.7 + - - -
69B ASP* 3.6 34.1 - - + -
74B SER* 3.8 15.5 - - - -
104B LEU* 1.3 74.5 - - - +
106B TYR* 1.3 67.8 + - - +
107B GLY* 3.6 16.8 - - - -
111B ALA* 3.8 11.7 - - + -
151B TYR* 4.6 0.4 - - - -
169B TYR* 3.6 28.7 - + + -
174B TYR* 3.2 42.2 - + + -
----------------------------------------------------------
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