Contacts of the helix formed by residues 109 - 116 (chain C) in PDB entry 6V99
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 GLY 109 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLN* 6.0 0.9 - - - -
107C TYR* 3.1 9.2 + - - +
108C GLU* 1.3 78.3 - - - +
110C THR* 1.3 61.9 + - - -
112C ASP* 3.1 3.1 + - - +
113C ALA* 2.9 27.1 + - - +
230C SER 4.1 0.9 - - - -
231C ARG 3.1 13.9 - - - -
232C ASP* 3.8 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 3.6 33.6 - - + +
109C GLY* 1.3 72.5 - - - -
111C ALA* 1.3 60.5 + - - +
113C ALA* 3.4 19.6 + - - +
114C VAL* 3.7 4.7 + - - +
232C ASP* 2.8 21.4 + - - +
233C PHE* 2.7 47.9 + - - +
234C GLY 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C THR* 1.3 78.7 + - - +
112C ASP* 1.3 61.5 + - - +
114C VAL* 3.1 2.9 + - - -
115C TYR* 2.9 27.1 + - - +
220C LEU* 3.6 15.0 - - + +
223C ASP* 4.0 9.6 - - - +
231C ARG* 2.8 21.2 + - - +
232C ASP 3.8 2.5 - - - +
233C PHE* 3.8 10.7 - - + +
237C ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TRP 4.5 1.6 - - - +
107C TYR* 3.7 7.8 - - - -
108C GLU* 2.9 39.8 + - + +
109C GLY 3.1 13.3 + - - +
111C ALA* 1.3 78.7 - - - +
113C ALA* 1.3 56.7 + - - +
115C TYR* 3.6 1.5 - - - -
116C GLN* 2.8 63.0 + - - +
231C ARG* 2.8 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 2.7 26.0 + - - -
18C LEU* 4.3 9.0 - - + -
65C ALA* 4.0 15.0 - - + +
67C GLN* 5.9 0.4 - - - +
107C TYR* 3.6 28.4 - - + -
109C GLY 2.9 12.0 + - - +
110C THR* 3.5 15.7 - - - +
111C ALA 3.1 0.6 - - - -
112C ASP* 1.3 77.4 - - - +
114C VAL* 1.3 51.4 + - - +
117C ASN* 3.0 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 3.7 30.7 - - + -
18C LEU* 4.5 2.9 - - + -
110C THR 3.7 14.4 - - - +
111C ALA 3.1 2.4 + - - +
112C ASP 3.1 0.2 - - - -
113C ALA* 1.3 76.2 - - - +
115C TYR* 1.3 67.6 + - - +
116C GLN 3.2 1.8 - - - -
117C ASN* 2.9 14.6 + - - +
118C ILE* 3.3 9.4 + - - +
121C ILE* 3.7 22.9 - - + -
129C MET* 4.7 2.7 - - + -
131C ILE* 4.4 4.3 - - + -
216C LEU* 4.6 11.0 - - + -
217C MET* 4.8 0.4 - - + -
220C LEU* 3.7 22.9 - - + -
233C PHE* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ALA 2.9 16.6 + - - +
112C ASP* 3.6 8.7 - - - +
114C VAL* 1.3 76.7 - - - +
116C GLN* 1.3 77.2 + - - +
117C ASN 3.0 1.6 + - - -
118C ILE* 3.2 35.8 + - + +
220C LEU* 4.0 18.3 - - + +
221C ARG* 4.2 20.4 - - + -
224C ALA* 3.5 27.1 - - + +
231C ARG* 3.3 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG* 4.2 14.5 + - - +
101C VAL* 5.4 5.7 - - - +
102C SER* 4.6 21.7 + - - +
106C TRP 6.1 0.2 - - - +
107C TYR* 3.6 24.5 - - + -
108C GLU* 5.8 0.6 - - - +
112C ASP* 2.8 50.7 + - - +
115C TYR* 1.3 94.1 - - - +
117C ASN* 1.3 61.7 + - - +
118C ILE 3.5 0.6 + - - -
119C ASP* 3.7 10.2 - - - +
231C ARG* 4.9 2.0 - - - +
----------------------------------------------------------
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