Contacts of the helix formed by residues 89 - 99 (chain B) in PDB entry 3COG
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 SER 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLY* 2.5 32.0 + - - -
246A VAL* 5.0 1.6 - - - -
87B PHE* 3.1 2.8 - - - +
88B ALA* 1.3 79.8 - - - +
90B GLY* 1.3 58.8 + - - +
91B LEU* 3.5 5.5 + - - -
92B ALA* 2.8 21.8 + - - +
93B ALA 3.0 23.4 + - - -
221B VAL* 3.7 16.8 - - - -
222B MET* 3.7 4.3 - - - +
223B GLY* 3.3 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 1.3 73.7 - - - +
91B LEU* 1.3 56.5 + - - +
93B ALA* 3.2 5.4 + - - +
94B THR* 2.9 31.9 + - - -
114B TYR* 6.2 1.8 - - - -
207B MET* 3.5 6.9 - - - +
208B TYR 3.8 20.4 - - - -
209B SER* 4.1 16.5 + - - +
211B THR* 5.3 0.6 + - - -
221B VAL* 5.4 0.2 - - - +
222B MET 3.7 4.0 + - - +
223B GLY* 3.7 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASN 3.5 24.5 - - - +
242A SER 3.7 16.2 - - - +
243A LEU 3.5 6.7 - - - +
244A GLY* 4.1 4.0 - - - -
89B SER* 3.7 8.9 - - - +
90B GLY* 1.3 75.7 - - - +
92B ALA* 1.3 56.1 + - - +
94B THR* 3.2 8.9 + - - +
95B VAL* 2.9 33.1 + - - +
114B TYR* 4.4 21.8 - - + +
116B GLY* 3.4 33.9 - - - +
117B THR* 4.2 3.8 - - - +
119B ARG* 3.7 16.2 - - - +
120B TYR* 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU 3.3 11.4 + - - +
244A GLY 3.5 11.0 - - - +
87B PHE* 4.3 2.7 - - + -
88B ALA* 4.3 0.7 - - + +
89B SER* 2.8 32.3 + - - +
91B LEU* 1.3 73.2 - - - +
93B ALA* 1.3 54.4 + - - +
95B VAL* 3.9 3.7 - - - +
96B THR* 2.8 37.2 + - - -
245B ALA* 3.5 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.9 20.5 - - + +
89B SER 3.0 13.1 + - - +
90B GLY* 3.2 14.1 - - - +
92B ALA* 1.3 75.9 - - - +
94B THR* 1.3 51.6 + - - +
96B THR* 3.2 2.6 + - - -
97B ILE* 2.8 40.8 + - - +
207B MET* 4.3 9.6 - - + -
208B TYR 4.6 0.2 - - - +
223B GLY* 4.4 7.0 - - - -
224B LEU 4.5 1.1 - - - +
225B VAL* 3.8 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY 2.9 15.1 + - - -
91B LEU* 3.5 13.9 - - + +
93B ALA* 1.3 76.0 - - - +
95B VAL* 1.3 57.2 + - - +
97B ILE* 3.2 3.3 + - - +
98B THR* 2.9 32.6 + - - -
117B THR* 4.4 15.5 + - + +
120B TYR* 4.0 19.7 - - + -
121B PHE* 4.2 12.3 - - + -
155B TRP* 3.4 41.0 - - + -
207B MET* 3.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 5.5 3.8 - - + -
99A HIS* 4.8 3.6 - - + +
242A SER 4.7 0.9 - - - +
243A LEU* 3.7 38.4 - - + +
91B LEU 2.9 20.8 + - - +
92B ALA* 3.9 5.4 - - - +
94B THR* 1.3 74.9 - - - +
96B THR* 1.3 64.5 + - - +
98B THR* 3.2 2.4 + - - -
99B HIS* 2.9 45.4 + - + +
120B TYR* 3.6 41.5 - - + +
243B LEU* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.3 38.8 - - + -
92B ALA 2.8 21.6 + - - -
93B ALA 3.6 4.0 - - - -
95B VAL* 1.3 76.3 - - - +
97B ILE* 1.3 63.7 + - - +
99B HIS* 3.2 15.8 + - - +
100B LEU* 4.5 0.3 - - - +
236B LEU* 4.3 9.1 - - + +
239B LEU* 3.5 37.6 + - + +
240B GLN 4.2 0.4 - - - +
243B LEU* 4.0 16.8 - - + +
245B ALA* 4.5 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA 2.8 21.1 + - - +
94B THR 3.5 3.6 - - - +
96B THR* 1.3 75.8 - - - +
98B THR* 1.3 59.6 + - - +
100B LEU* 2.9 37.1 + - + +
101B LEU* 4.9 1.9 - - - +
153B LEU* 4.2 13.1 - - + +
155B TRP* 3.9 35.4 - - + -
185B VAL* 4.1 13.0 - - + -
205B ILE* 4.1 23.3 - - + -
207B MET* 4.1 7.2 - - + -
225B VAL* 3.9 22.2 - - + -
236B LEU* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 4.4 4.1 - - + -
94B THR* 2.9 18.6 + - - +
95B VAL 3.2 1.1 + - - -
97B ILE* 1.3 77.5 - - - +
99B HIS* 1.3 57.6 + - - +
101B LEU* 3.1 29.2 + - - +
107B ILE* 4.0 15.2 - - + +
120B TYR* 3.2 39.3 - - + +
121B PHE* 3.4 15.4 - - - -
125B ALA* 4.2 2.2 - - + -
130B LEU* 3.6 25.1 - - + -
153B LEU* 4.7 5.7 - - - +
155B TRP* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.9 0.7 - - + -
99A HIS* 3.6 36.1 + + - -
120A TYR* 4.8 4.6 + - - -
124A VAL* 3.5 28.3 - - + +
125A ALA* 6.3 0.2 - - - -
128A PHE* 3.7 27.1 - + - -
95B VAL* 2.9 36.3 + - + +
96B THR 3.2 10.7 + - - +
98B THR* 1.3 74.3 - - + +
100B LEU* 1.3 60.8 + - - +
101B LEU 3.2 7.5 + - - +
120B TYR* 4.3 6.1 + - - -
239B LEU* 3.4 24.0 - - + +
243B LEU* 3.6 24.9 - - + +
----------------------------------------------------------
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