Contacts of the helix formed by residues 105 - 120 (chain B) in PDB entry 1GZ0
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 105 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 3.5 2.6 - - - +
104B THR* 1.3 79.5 + - - +
106B PRO* 1.3 72.2 - - - +
107B HIS* 2.8 27.7 + - - +
108B ASN* 2.9 36.5 + - - +
109B LEU* 3.1 10.0 + - - +
132B ALA* 3.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B THR 3.6 8.3 - - - +
105B ASP* 1.3 89.1 - - - +
107B HIS* 1.3 56.0 + - - +
109B LEU* 3.2 3.0 + - + +
110B GLY 2.9 25.1 + - - -
132B ALA* 3.9 11.6 - - + -
133B GLN* 4.3 7.4 - - + +
135B ASN* 3.4 35.7 - - - +
137B THR* 4.4 7.2 - - + -
138B ALA* 3.2 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 2.8 16.2 + - - +
106B PRO* 1.3 79.7 - - - +
108B ASN* 1.3 64.2 + - - +
110B GLY 3.5 0.2 + - - -
111B ALA* 2.9 30.1 + - + +
137B THR* 4.6 11.3 - - + +
141B VAL* 3.6 37.1 - - + +
107G HIS* 5.6 10.4 - + - -
226G ASN* 5.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 3.7 17.9 - - + +
105B ASP* 2.9 28.8 + - - +
107B HIS* 1.3 80.9 + - - +
109B LEU* 1.3 56.4 + - - +
111B ALA* 3.5 0.3 - - - +
112B CYS* 2.7 42.6 + - - +
198B GLU* 5.8 1.4 + - - -
226B ASN* 3.7 21.5 + - - +
227B VAL* 5.0 17.9 - - + +
228B SER* 3.8 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.0 21.5 - - + -
103B VAL* 3.6 13.1 - - + +
105B ASP 3.1 11.0 + - - +
106B PRO* 3.5 9.2 - - + +
108B ASN* 1.3 77.2 - - - +
110B GLY* 1.3 62.8 + - - +
112B CYS* 3.2 3.6 + - - +
113B LEU* 3.0 35.8 + - + +
124B VAL* 5.1 0.7 - - + -
126B VAL* 4.8 4.3 - - + -
132B ALA* 3.9 28.0 - - + +
133B GLN 4.0 5.4 - - - +
134B LEU* 3.9 24.7 - - + +
138B ALA* 4.5 2.0 - - + -
151B LEU* 4.2 29.8 - - + -
153B ARG* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO 2.9 13.9 + - - -
107B HIS 3.9 1.1 - - - -
109B LEU* 1.3 76.9 - - - +
111B ALA* 1.3 56.8 + - - +
113B LEU* 2.9 26.1 + - - +
114B ARG* 3.0 11.1 + - - +
138B ALA* 3.3 30.0 - - - +
141B VAL* 3.8 6.1 - - - -
142B ALA* 3.5 8.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B HIS* 2.9 27.1 + - + +
108B ASN* 3.5 1.3 - - - +
110B GLY* 1.3 74.4 - - - +
112B CYS* 1.3 59.4 + - - +
114B ARG* 3.6 9.4 + - - +
115B SER* 3.3 24.4 + - - -
141B VAL* 3.3 14.9 - - + +
228B SER* 2.8 30.5 - - - +
226G ASN* 6.2 3.8 - - + -
229G VAL* 5.4 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.3 7.8 - - + +
100B LEU* 3.9 30.1 - - + -
103B VAL* 5.0 2.5 - - - -
108B ASN* 2.7 25.9 + - - +
109B LEU 3.6 4.7 - - - +
110B GLY 3.1 0.2 - - - -
111B ALA* 1.3 71.9 - - - +
113B LEU* 1.3 58.3 + - - +
115B SER* 3.4 6.9 + - - -
116B ALA* 2.8 28.1 + - - +
124B VAL* 6.2 0.2 - - + -
227B VAL* 4.3 5.8 - - - -
228B SER* 4.2 14.1 - - - +
231B THR* 3.6 33.7 - - + -
235B LEU* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.0 26.1 + - + +
110B GLY* 2.9 9.5 + - - +
112B CYS* 1.3 72.9 - - + +
114B ARG* 1.3 69.6 + - - +
116B ALA* 2.9 6.0 + - - +
117B ASP 2.7 21.3 + - - -
124B VAL* 3.9 32.8 - - + -
134B LEU* 3.7 31.9 - - + -
142B ALA* 4.1 13.7 - - + -
145B ALA* 3.4 17.3 - - + +
146B ALA* 4.3 7.9 - - - -
149B VAL* 4.4 21.1 - - + +
151B LEU* 4.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLY 3.0 9.9 + - - +
111B ALA* 3.6 11.9 - - - +
113B LEU* 1.3 78.1 - - - +
115B SER* 1.3 58.3 + - - +
117B ASP* 3.2 2.9 + - - +
118B ALA* 2.9 28.3 + - - +
141B VAL* 3.7 17.9 + - - +
142B ALA 3.6 13.5 - - - +
143B CYS* 3.9 27.9 - - + +
145B ALA* 3.7 11.6 - - - +
198G GLU* 3.0 28.9 + - - -
222G VAL* 3.7 14.5 - - + +
224G SER* 2.9 38.9 + - - +
225G LEU* 3.3 10.0 + - + -
226G ASN* 3.6 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA 3.3 12.2 + - - -
112B CYS* 3.7 9.9 - - - -
113B LEU 3.2 0.4 - - - -
114B ARG* 1.3 77.2 - - - +
116B ALA* 1.3 57.2 + - - +
118B ALA* 3.3 1.9 + - - +
119B ALA* 2.9 30.8 + - - +
228B SER 4.6 2.3 + - - -
231B THR* 5.1 0.9 - - - -
232B GLY* 4.4 14.5 - - - -
235B LEU* 4.1 14.5 - - - +
236B PHE* 4.1 5.0 - - - -
225G LEU* 4.2 13.8 - - - +
229G VAL* 3.6 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.0 7.2 - - + -
112B CYS 2.8 16.3 + - - +
113B LEU* 2.9 9.2 + - - +
115B SER* 1.3 76.8 - - - +
117B ASP* 1.3 61.7 + - - +
119B ALA* 3.2 1.9 + - - +
120B GLY 3.0 18.2 + - - -
121B VAL* 3.0 24.4 + - + +
124B VAL* 3.8 28.5 - - + -
149B VAL* 4.7 4.5 - - + -
235B LEU* 4.1 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU 2.7 8.7 + - - -
114B ARG 3.6 3.8 - - - +
116B ALA* 1.3 73.7 - - - +
118B ALA* 1.3 62.3 + - - +
120B GLY* 3.3 11.1 + - - -
121B VAL 5.0 1.6 - - - +
145B ALA* 3.4 23.1 - - + -
148B SER* 3.0 24.9 + - - +
149B VAL* 3.6 15.5 - - + +
220G GLY* 3.5 16.3 + - - -
221G SER* 2.8 17.2 + - - -
222G VAL* 2.7 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG 2.9 11.3 + - - +
115B SER 3.7 3.4 - - - +
117B ASP* 1.3 80.2 + - - +
119B ALA* 1.3 60.3 + - - +
236B PHE* 3.9 12.2 - - + -
239B VAL* 5.0 0.7 - - - +
217G PRO 4.1 1.0 - - - +
218G MSE 3.6 21.3 - - + -
219G ALA* 3.0 28.7 + - - +
220G GLY 4.5 1.1 - - - +
222G VAL* 4.9 4.5 - - + -
225G LEU* 3.4 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 3.7 11.2 - - + -
115B SER 2.9 17.5 + - - +
116B ALA 3.6 4.9 - - - +
118B ALA* 1.3 77.2 - - - +
120B GLY* 1.3 60.5 + - - +
121B VAL* 4.3 5.4 - - + -
235B LEU* 3.7 25.6 - - + -
236B PHE* 4.1 7.2 - - + -
239B VAL* 3.4 33.6 - - + +
219G ALA* 4.1 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 3.7 16.8 - - - +
116B ALA 3.0 3.0 + - - -
117B ASP 3.3 11.4 + - - -
118B ALA 3.3 0.2 - - - -
119B ALA* 1.3 80.8 - - - +
121B VAL* 1.3 64.2 + - - +
122B HIS* 3.7 12.4 + - - -
219G ALA* 4.2 13.2 - - - -
220G GLY* 5.9 0.2 - - - -
----------------------------------------------------------
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