Contacts of the helix formed by residues 115 - 123 (chain C) in PDB entry 3GZN
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 115 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 4.4 2.0 - - - -
69C GLY* 4.2 14.5 - - - +
70C ASN* 6.2 0.7 - - - -
113C GLU 3.9 0.8 + - - -
114C GLU* 1.3 75.1 - - - +
116C PRO* 1.4 67.3 - - - +
117C GLU* 3.5 8.3 + - - +
118C ASN* 3.1 31.4 + - - +
119C LEU* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.8 35.0 - - + -
44C ASN* 5.1 7.4 - - - +
67C ILE* 3.9 18.1 - - + -
68C ASP* 5.2 0.4 - - - -
69C GLY 5.0 4.9 - - - +
70C ASN* 6.3 0.9 - - - +
115C SER* 1.4 86.7 - - - +
117C GLU* 1.3 62.5 + - + +
119C LEU* 3.6 7.6 + - + +
120C LEU* 3.2 32.1 + - + +
127C PHE* 4.9 5.0 - - + -
138C LEU* 4.4 9.9 - - + -
142C THR* 4.2 16.8 - - + -
146C LEU* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C SER* 3.2 7.2 + - - +
116C PRO* 1.3 76.8 - - + +
118C ASN* 1.3 66.3 + - - +
120C LEU* 3.2 4.6 + - - -
121C ASP* 3.1 30.4 + - - +
141C SER* 4.2 6.6 + - - -
142C THR* 2.9 44.8 + - + +
145C ARG* 2.9 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 4.4 11.4 - - + +
115C SER* 3.1 30.8 + - - +
117C GLU* 1.3 73.5 - - - +
119C LEU* 1.3 67.0 + - - +
121C ASP* 3.2 9.5 + - - +
122C ASN* 3.0 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 4.6 7.9 - - + -
112C VAL* 4.0 16.8 - - + -
114C GLU* 3.6 31.2 - - + +
115C SER 2.9 12.5 + - - +
116C PRO* 3.6 10.3 - - + +
117C GLU 3.3 0.2 - - - -
118C ASN* 1.3 76.8 - - - +
120C LEU* 1.3 57.2 + - - +
122C ASN* 5.2 1.1 - - - -
123C ASP* 2.7 66.2 + - + +
124C PRO* 4.9 0.2 - - - -
126C PHE* 3.7 31.9 - - + -
127C PHE* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PRO* 3.2 20.5 + - + +
117C GLU* 3.2 6.3 + - - +
119C LEU* 1.3 77.6 - - - +
121C ASP* 1.3 58.2 + - - +
124C PRO* 3.2 27.8 - - + +
127C PHE* 3.5 24.9 - - + -
142C THR* 4.7 4.9 - - + +
145C ARG* 3.2 57.9 + - + +
146C LEU* 3.9 21.3 - - + +
149C VAL* 3.9 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU* 3.1 16.0 + - - +
118C ASN* 3.6 13.4 - - - +
120C LEU* 1.3 77.9 - - - +
122C ASN* 1.3 71.7 + - - +
124C PRO* 5.0 2.1 - - - +
145C ARG* 2.6 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ASN* 3.0 29.9 + - - +
119C LEU* 5.0 0.7 - - - -
121C ASP* 1.3 94.8 - - - +
123C ASP* 1.3 62.5 + - + +
124C PRO* 3.9 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 2.7 32.3 + - + +
122C ASN* 1.3 77.4 - - + +
124C PRO* 1.4 63.1 - - - +
125C SER* 3.1 24.1 + - - -
126C PHE* 3.0 42.8 + - - +
127C PHE* 4.8 0.9 - - - -
129C ARG* 5.2 3.3 + - - -
----------------------------------------------------------
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