Contacts of the helix formed by residues 78 - 90 (chain B) 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 GLY 78 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY* 3.4 4.9 + - - -
77B ALA* 1.3 78.5 - - - +
79B GLY* 1.3 60.5 + - - +
80B LEU 3.5 1.6 - - - -
81B GLY* 3.6 2.9 - - - +
82B CYS* 2.8 35.9 + - - -
100B ASP* 3.6 1.8 + - - -
112B GLN* 3.3 16.8 - - - -
464I B39 3.3 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY* 1.3 72.4 - - - +
80B LEU* 1.3 62.4 + - - +
82B CYS* 4.1 2.6 - - - +
83B GLU* 3.6 18.2 + - - +
111B ARG* 4.3 18.9 - - - +
112B GLN* 3.4 18.6 - - - +
113B PHE* 5.4 0.5 - - - -
317B ASN* 4.1 15.8 - - - +
76I GLY 3.9 1.3 - - - -
464I B39 2.7 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 1.3 73.0 - - - +
81B GLY* 1.3 62.9 + - - +
83B GLU* 3.4 4.8 + - - +
84B LEU* 3.0 29.9 + - + +
165B GLY* 3.8 20.9 - - - -
201B GLY* 3.5 35.0 - - - +
202B GLY* 3.9 7.4 - - - +
203B THR* 4.8 0.9 - - + -
317B ASN* 3.6 26.6 + - - +
320B ILE* 3.7 11.9 - - + -
321B ALA* 3.6 36.1 - - + +
324B CYS* 5.7 0.7 - - - -
76I GLY* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.4 0.8 - - - +
76B GLY 3.0 29.1 - - - -
77B ALA* 4.5 2.5 - - - -
78B GLY 3.3 10.7 + - - +
80B LEU* 1.3 76.7 - - - +
82B CYS* 1.3 63.2 + - - +
84B LEU* 3.0 22.5 + - - +
85B LEU* 3.0 17.7 + - - +
165B GLY 4.8 3.1 + - - -
76I GLY 4.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA* 3.6 15.5 - - - +
78B GLY 2.8 23.1 + - - +
79B GLY 4.1 2.5 - - - +
81B GLY* 1.3 70.5 - - - +
83B GLU* 1.3 62.7 + - - +
85B LEU* 3.3 7.5 + - - +
86B LYS* 3.1 22.2 + - - +
112B GLN* 4.2 6.3 - - - -
113B PHE* 3.8 19.7 - - + +
114B LEU* 3.8 47.6 - - + +
115B PHE* 3.9 15.5 - - - -
128B ALA* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 3.8 1.9 - - - +
54A LYS* 2.8 40.5 + - - -
502A ALA* 5.3 1.0 - - + +
79B GLY 3.6 10.8 + - - +
80B LEU* 3.4 4.2 + - - +
81B GLY 3.2 0.4 - - - -
82B CYS* 1.3 76.8 - - - +
84B LEU* 1.3 59.7 + - - +
86B LYS* 3.1 18.5 + - - +
87B ASN* 2.9 43.6 + - - +
111B ARG 5.2 1.7 - - - +
113B PHE* 3.5 16.6 - - - -
314B ALA* 4.5 4.0 - - - +
317B ASN* 4.6 3.0 - - - +
318B ALA* 3.7 27.0 + - - +
321B ALA* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.0 26.7 - - + -
80B LEU* 3.0 22.6 + - + +
81B GLY* 3.0 7.9 + - - +
83B GLU* 1.3 74.6 - - - +
85B LEU* 1.3 54.4 + - - +
87B ASN* 3.1 4.9 + - - +
88B LEU* 2.8 44.2 + - + +
163B VAL* 3.8 24.0 - - + -
164B CYS 4.3 1.1 - - - -
165B GLY* 4.1 22.0 - - - +
321B ALA* 3.5 28.0 - - + +
324B CYS* 3.7 21.5 - - + -
325B ALA* 4.4 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.3 7.2 - - + +
77B ALA* 5.0 2.9 - - + -
81B GLY 3.0 17.1 + - - +
82B CYS* 3.4 9.0 - - - +
84B LEU* 1.3 75.1 - - - +
86B LYS* 1.3 62.1 + - - +
88B LEU* 4.2 3.3 - - - +
89B ALA* 3.2 25.5 + - - +
96B ILE* 3.7 27.3 - - + +
98B VAL* 3.3 35.7 - - + -
114B LEU* 4.1 6.1 - - + -
128B ALA* 3.9 28.9 - - + +
132B LEU* 3.2 22.8 - - + +
141B VAL* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 3.0 26.1 + - - +
54A LYS* 4.4 3.1 - - + +
81A PHE* 3.6 44.9 - - + -
498A HIS* 2.9 21.5 + - - +
502A ALA* 4.0 4.0 - - - +
82B CYS 3.1 10.0 + - - +
83B GLU* 3.1 30.0 + - - +
85B LEU* 1.3 79.5 - - - +
87B ASN* 1.3 87.2 + - - +
89B ALA* 3.3 2.8 + - - +
90B LEU* 3.1 26.1 + - + +
113B PHE* 3.8 20.0 - - + -
114B LEU* 5.8 0.2 - - + -
132B LEU* 4.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A HIS* 3.4 13.2 - - - -
499A THR* 3.8 13.0 - - + +
502A ALA* 3.9 3.0 - - - +
83B GLU* 2.9 33.1 + - - +
84B LEU 3.5 2.9 - - - +
86B LYS* 1.3 104.5 + - - +
88B LEU* 1.3 61.5 + - - +
90B LEU* 3.6 1.2 + - - +
91B SER* 2.8 29.8 + - - -
321B ALA 3.4 29.5 + - - -
322B ALA* 3.5 10.3 - - - +
325B ALA* 3.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.8 20.9 - - + -
74B VAL* 3.6 31.2 - - + -
84B LEU* 2.8 25.4 + - + +
85B LEU* 4.3 0.9 - - - +
87B ASN* 1.3 70.3 - - - +
89B ALA* 1.3 65.5 + - - +
91B SER* 3.0 14.7 + - - -
92B GLY 3.3 0.3 + - - -
93B PHE* 3.0 36.2 + - + +
96B ILE* 3.8 17.9 - - + -
163B VAL* 4.6 5.4 - - + -
325B ALA* 4.2 18.4 - - + +
328B VAL* 3.9 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 3.5 20.1 - - - -
85B LEU 3.2 17.3 + - - +
86B LYS 3.3 3.8 + - - +
88B LEU* 1.3 79.7 - - - +
90B LEU* 1.3 62.2 + - - +
91B SER 3.4 0.3 + - - -
92B GLY 3.5 2.3 + - - -
93B PHE 3.7 14.5 - - - +
96B ILE* 4.0 3.7 - - + +
132B LEU* 3.9 16.2 - - + -
136B VAL* 4.0 15.0 - - + +
139B CYS* 3.8 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 5.0 2.5 - - - +
78A GLY 3.5 25.2 - - - +
79A ASN* 4.3 2.1 - - - +
80A ASN 4.1 10.5 - - - +
81A PHE* 3.9 29.4 - - + +
498A HIS* 3.3 53.7 - - + +
37B ARG* 6.0 0.7 - - - +
38B TRP* 3.7 15.5 - - + -
41B VAL* 4.1 8.0 - - - +
86B LYS* 3.1 15.5 + - + +
87B ASN 3.9 1.1 - - - +
89B ALA* 1.3 75.8 - - - +
91B SER* 1.3 58.4 + - - +
92B GLY 3.4 0.9 - - - -
136B VAL* 3.9 26.7 - - + -
----------------------------------------------------------
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