Contacts of the helix formed by residues 129 - 138 (chain G) in PDB entry 3ZWG
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 ASP 129 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G TYR* 3.7 18.1 - - + -
89G VAL* 5.4 0.2 - - - +
127G ARG* 4.0 7.7 - - + +
128G ALA* 1.3 76.3 - - - +
130G GLN* 1.3 70.2 + - - +
131G ARG* 3.4 19.4 - - - +
132G MET* 2.8 31.3 + - - +
133G TYR 3.0 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G TYR* 2.7 46.6 + - + +
53G ARG* 3.5 28.1 + - - +
129G ASP* 1.3 74.2 - - - +
131G ARG* 1.3 65.2 + - - +
133G TYR* 3.2 10.9 + - - +
134G GLU* 2.7 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G ASP* 3.4 19.9 - - - +
130G GLN* 1.3 81.8 - - - +
132G MET* 1.3 63.0 + - - +
134G GLU* 3.3 25.3 + - - +
135G GLU* 3.3 44.7 + - - +
139G HIS* 6.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G VAL* 3.7 23.1 - - + -
91G ALA* 5.1 1.8 - - - -
99G THR* 4.9 1.3 - - + -
101G ALA* 3.7 17.7 - - + -
122G TYR* 4.0 26.2 - - + +
126G LYS* 3.8 31.4 - - + +
127G ARG 3.7 19.7 - - - +
128G ALA* 4.0 7.6 - - - -
129G ASP* 2.8 24.6 + - - +
131G ARG* 1.3 71.5 - - + +
133G TYR* 1.3 66.5 + - - +
135G GLU* 3.2 12.5 + - - +
136G LEU* 2.9 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G TYR* 4.1 10.3 - - + -
53G ARG* 3.8 32.5 + - + +
87G VAL* 3.4 32.7 - - + +
88G GLY 5.4 1.3 - - - -
89G VAL* 3.8 20.9 - - + +
103G LEU* 4.2 10.8 - - + -
105G SER* 5.4 0.2 + - - -
129G ASP 3.0 10.5 + - - +
130G GLN* 3.4 28.9 - - - +
132G MET* 1.3 75.6 - - - +
134G GLU* 1.3 65.6 + - - +
136G LEU* 3.3 1.5 + - - +
137G TYR* 2.9 62.2 + + + +
138G TYR* 4.2 20.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G GLN* 2.7 51.7 + - - +
131G ARG* 3.4 27.0 + - - +
132G MET 3.2 0.2 - - - -
133G TYR* 1.3 79.9 - - + +
135G GLU* 1.3 63.8 + - + +
138G TYR* 2.9 50.0 + - + +
139G HIS* 3.6 9.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G TYR* 2.6 43.0 + - - +
126G LYS* 5.8 1.2 - - - -
131G ARG* 3.3 44.3 + - - +
132G MET* 3.2 12.2 + - - +
134G GLU* 1.3 75.1 - - - +
136G LEU* 1.3 63.5 + - - +
139G HIS* 3.1 21.1 + - + +
140G ARG* 3.0 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G VAL* 3.7 30.3 - - + -
101G ALA* 4.0 12.1 - - + -
103G LEU* 3.6 32.6 - - + +
118G ASN* 2.8 35.8 + - + +
120G ARG* 3.5 32.8 - - + +
122G TYR* 3.8 14.4 - - + +
132G MET* 2.9 29.9 + - + +
133G TYR* 3.9 3.1 - - - +
135G GLU* 1.3 75.1 - - - +
137G TYR* 1.3 60.4 + - - +
140G ARG* 4.1 5.6 - - + +
142G PRO* 3.5 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LEU* 3.8 13.5 - - + -
105G SER* 3.6 31.6 + - - -
107G PRO* 5.9 0.5 - - - +
113G TYR* 4.8 16.6 - - - +
114G SER 5.1 0.7 + - - -
116G TRP* 4.1 29.6 + + + -
133G TYR* 2.9 52.2 + + + +
134G GLU 4.2 0.7 - - - +
136G LEU* 1.3 73.9 - - - +
138G TYR* 1.3 93.8 + + + +
142G PRO* 3.4 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ARG* 5.5 4.0 + - - -
133G TYR* 4.2 17.4 + + - -
134G GLU* 2.9 50.9 + - + -
137G TYR* 1.3 104.3 - + + +
139G HIS* 1.3 81.4 + + + +
140G ARG 3.4 1.5 + - - -
141G SER* 3.7 8.5 + - - -
----------------------------------------------------------
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