Contacts of the helix formed by residues 120 - 130 (chain G) in PDB entry 3ZNI
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 VAL 120 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G HIS 4.0 9.6 - - - +
76G PRO 3.0 9.6 + - - +
78G ILE 3.7 17.7 - - - +
79G ASN* 3.7 29.2 - - + -
118G PRO* 4.2 2.5 - - - -
119G LEU* 1.3 80.1 - - + +
121G PRO* 1.3 65.9 - - + +
122G GLU* 4.3 8.5 - - + +
123G ILE* 3.2 29.7 + - + +
124G ALA* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G PRO* 4.2 20.4 - - + +
119G LEU 3.3 11.7 - - - +
120G VAL* 1.3 86.1 - - + +
122G GLU* 1.3 63.2 + - - +
124G ALA* 3.3 2.1 + - - +
125G ARG* 3.0 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 4.6 10.9 - - - +
133C LYS* 3.8 29.3 + - - +
74G TYR* 5.0 5.4 + - - -
120G VAL* 3.3 8.9 - - + -
121G PRO* 1.3 81.2 - - - +
123G ILE* 1.3 67.8 + - + +
125G ARG* 3.4 25.4 + - - +
126G ILE* 3.3 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G ILE 5.4 0.7 - - - +
74G TYR* 3.5 48.9 - - + +
75G HIS 3.6 22.9 - - - +
76G PRO* 3.6 16.6 - - + -
78G ILE 5.0 2.0 - - - +
120G VAL* 3.2 27.6 + - + +
122G GLU* 1.3 81.3 - - + +
124G ALA* 1.3 57.1 + - - +
126G ILE* 3.3 2.9 + - - +
127G TYR* 2.9 27.9 + - - +
134G TYR* 3.5 27.0 - - + -
141G TRP* 5.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G PRO* 4.3 7.1 - - + +
115G PRO* 3.5 30.3 - - + +
118G PRO* 3.6 24.9 - - + -
120G VAL 3.1 6.2 + - - +
121G PRO 3.5 8.3 - - - +
122G GLU 3.3 0.2 - - - -
123G ILE* 1.3 75.7 - - - +
125G ARG* 1.3 63.3 + - + +
127G TYR* 3.1 10.4 + - - +
128G LYS* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 4.9 24.0 + - - +
126C ILE* 6.1 1.2 - - - +
129C THR* 3.3 47.3 + - - +
130C ASP* 5.2 5.9 - - - +
121G PRO* 3.0 28.2 + - - +
122G GLU* 3.6 34.4 + - - +
123G ILE 3.4 0.2 - - - -
124G ALA* 1.3 75.9 - - + +
126G ILE* 1.3 53.9 + - + +
128G LYS* 3.1 10.1 + - - +
129G THR* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 5.8 4.0 - - - +
133C LYS* 5.5 4.7 - - - +
74G TYR* 3.5 22.9 - - - +
122G GLU* 3.3 28.1 + - + +
123G ILE 3.7 6.1 - - - +
124G ALA 3.3 0.2 - - - -
125G ARG* 1.3 77.1 - - + +
127G TYR* 1.3 59.8 + - - +
129G THR* 3.8 6.3 - - - +
130G ASP* 2.8 41.4 + - + +
133G LYS* 4.0 38.8 - - + +
134G TYR* 3.6 30.5 - - + +
137G ILE* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G PRO* 4.4 4.5 - - + -
111G CYS 4.9 3.3 + - - -
113G PRO* 3.5 35.3 - - + +
115G PRO* 3.8 28.0 - - + -
123G ILE 2.9 14.8 + - - +
124G ALA* 3.4 12.6 - - - +
126G ILE* 1.3 77.1 - - - +
128G LYS* 1.3 61.6 + - + +
131G ARG* 3.1 73.2 + - - +
134G TYR* 3.4 50.5 - + + -
135G ASN* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G PRO* 3.8 34.9 + - + -
116G ASP* 3.0 30.5 + - - +
124G ALA* 2.9 20.6 + - - +
125G ARG* 3.7 7.0 - - - +
127G TYR* 1.3 80.4 - - + +
129G THR* 1.3 64.9 + - + +
131G ARG* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 3.3 52.0 + - - +
125G ARG* 2.8 31.6 + - + +
126G ILE* 3.8 3.8 - - - -
128G LYS* 1.3 81.3 - - + +
130G ASP* 1.3 64.7 + - - +
131G ARG 4.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLU* 4.4 9.0 - - - +
125C ARG* 5.7 3.1 - - - +
126G ILE* 2.8 20.0 + - + +
129G THR* 1.3 80.5 + - - +
131G ARG* 1.3 62.6 + - - +
132G GLU* 3.0 15.0 + - - +
133G LYS* 3.3 39.0 + - + +
134G TYR 3.0 16.8 + - - -
----------------------------------------------------------
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