Contacts of the helix formed by residues 114 - 124 (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 TYR 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY* 6.2 0.9 - - - -
91B LEU* 4.4 23.4 - - + +
113B VAL* 1.3 73.6 - - - +
115B GLY* 1.3 66.1 + - - +
116B GLY* 3.6 24.1 - - - -
117B THR* 2.8 45.7 + - - +
118B ASN 3.0 9.9 + - - -
119B ARG* 5.4 1.0 + - - -
157B GLU* 3.0 28.1 + - - +
187B ASP* 4.8 7.2 - - - +
190B PHE* 5.9 6.3 - + + -
209B SER* 6.2 3.8 - - - -
212B LYS* 4.8 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL 3.3 4.5 + - - -
114B TYR* 1.3 77.3 - - - +
116B GLY* 1.3 52.1 + - - +
118B ASN* 3.4 8.8 + - - +
119B ARG* 2.7 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A SER 4.9 0.2 - - - +
91B LEU* 3.4 20.8 - - - +
114B TYR* 3.2 26.5 - - - -
115B GLY* 1.3 75.4 - - - +
117B THR* 1.3 56.5 + - - +
119B ARG* 3.8 26.7 - - - +
120B TYR* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.7 3.2 - - - +
94B THR* 4.4 15.6 + - + -
113B VAL* 3.7 22.5 - - + +
114B TYR* 2.8 27.5 + - - +
116B GLY* 1.3 73.3 - - - +
118B ASN* 1.3 68.0 + - - +
120B TYR* 3.3 4.9 + - - +
121B PHE* 3.0 57.0 + - + -
155B TRP* 3.8 18.7 + - + +
187B ASP* 4.8 3.1 + - - -
207B MET* 5.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP 5.1 3.1 - - - +
113B VAL* 3.6 19.7 - - + +
114B TYR 3.0 6.8 + - - +
115B GLY* 3.6 11.7 + - - +
117B THR* 1.3 76.6 - - - +
119B ARG* 1.3 66.0 + - - +
121B PHE* 3.9 0.9 - - - +
122B ARG* 2.9 64.3 + - - +
134B PHE* 3.1 25.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 4.2 15.9 - - + -
241A ASN* 3.9 16.1 + - - +
242A SER* 3.2 28.3 + - - +
91B LEU* 3.7 27.1 - - - +
114B TYR* 5.4 1.4 + - - -
115B GLY 2.7 24.4 + - - +
116B GLY* 3.8 21.2 + - - +
118B ASN* 1.3 78.1 - - - +
120B TYR* 1.3 58.3 + - - +
122B ARG* 4.8 0.2 - - - -
123B GLN* 2.9 53.3 + - + +
124B VAL* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A HIS* 5.0 3.1 + + - -
242A SER* 4.2 12.8 - - - +
243A LEU* 3.5 33.7 - - + -
91B LEU* 4.8 3.6 - - + -
94B THR* 4.0 14.4 - - + -
95B VAL* 3.6 32.6 + - + +
98B THR* 3.2 46.2 - - + +
99B HIS* 4.3 6.8 + - - -
116B GLY 3.1 18.1 + - - +
117B THR* 3.3 3.6 + - - +
119B ARG* 1.3 78.5 - - - +
121B PHE* 1.3 70.1 + + - +
124B VAL* 3.0 29.6 + - + -
125B ALA* 2.9 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 4.2 3.1 - - + -
98B THR* 3.4 24.2 - - - -
107B ILE* 4.2 27.6 - - + -
109B CYS* 3.6 33.2 - - + -
117B THR* 3.0 47.0 + - + +
118B ASN 3.9 2.0 - - - +
120B TYR* 1.3 90.6 - + - +
122B ARG* 1.3 64.3 + - - +
125B ALA* 3.9 5.8 - - + -
126B SER* 3.1 23.6 + - - -
132B ILE* 3.4 28.6 - - + +
134B PHE* 4.3 4.0 - + + -
153B LEU* 4.6 1.3 - - + -
155B TRP* 3.9 25.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 2.9 46.0 + - - +
119B ARG* 4.2 1.1 - - - +
121B PHE* 1.3 77.2 - - - +
123B GLN* 1.3 76.2 + - + +
126B SER* 2.4 25.7 + - - -
127B GLU* 5.5 0.3 - - - +
132B ILE* 5.2 2.5 - - + -
134B PHE* 3.4 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 4.2 23.1 - - + -
603A GOL 3.9 6.6 - - - -
119B ARG* 2.9 33.8 + - + +
122B ARG* 1.3 95.8 - - + +
124B VAL* 1.3 61.5 + - + +
126B SER* 4.2 2.2 - - - -
127B GLU* 3.8 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A HIS* 3.6 30.5 - - + -
238A PHE* 4.1 23.6 - - + -
239A LEU* 4.1 11.9 - - + -
242A SER* 4.5 9.6 - - - -
243A LEU* 3.9 12.1 - - + -
603A GOL 3.7 17.0 - - - +
119B ARG 4.6 0.2 - - - +
120B TYR* 3.0 24.5 + - + +
122B ARG 3.6 0.2 - - - -
123B GLN* 1.3 84.3 - - + +
125B ALA* 1.3 67.6 + - - +
126B SER 3.2 0.7 - - - -
127B GLU* 2.9 20.8 + - - +
128B PHE* 3.4 9.0 - - + -
----------------------------------------------------------
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