Contacts of the helix formed by residues 112 - 129 (chain A) in PDB entry 1GG3
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 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A CYS* 1.3 77.4 - - - +
113A PHE* 1.3 59.8 + - - +
114A ALA* 3.6 8.0 + - - +
115A THR* 2.7 33.8 + - - -
116A LEU* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 1.3 72.6 - - - +
114A ALA* 1.3 69.9 + - - +
116A LEU* 3.6 8.4 - - + +
117A ALA* 3.0 21.8 + - + +
149A ASN* 5.7 3.1 - - - -
151A THR* 3.8 9.2 - - - -
153A GLU* 3.2 38.8 - - + -
154A LEU* 3.2 49.1 - - + +
157A LYS* 4.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 3.3 7.5 + - - +
113A PHE* 1.3 79.2 - - - +
115A THR* 1.3 56.1 + - - +
117A ALA* 2.9 7.5 + - - +
118A LEU* 2.8 35.4 + - - +
157A LYS* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A CYS* 3.7 23.0 - - + +
112A SER* 2.7 22.0 + - - -
114A ALA* 1.3 77.5 - - - +
116A LEU* 1.3 62.1 + - - +
118A LEU* 3.2 8.7 + - + +
119A LEU* 2.9 51.6 + - + +
180A ASN* 5.4 5.2 - - + +
184A LEU* 3.9 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 3.9 14.6 - - + -
111A CYS* 3.7 28.9 - - - +
112A SER 3.0 25.8 + - - +
113A PHE* 3.6 8.7 - - + +
114A ALA 3.2 0.2 - - - -
115A THR* 1.3 76.4 - - - +
117A ALA* 1.3 53.1 + - - +
119A LEU* 3.9 3.3 - - - +
120A GLY* 2.7 34.7 + - - -
146A LEU* 3.5 26.3 - - - +
147A ALA* 3.7 22.0 - - + -
148A PRO* 4.4 5.8 - - + -
149A ASN* 3.8 13.9 - - - +
154A LEU* 4.2 16.0 - - + +
158A VAL* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.0 14.3 + - + +
114A ALA* 2.9 5.3 + - - +
116A LEU* 1.3 73.5 - - - +
118A LEU* 1.3 68.8 + - - +
121A SER* 3.1 11.8 + - - -
154A LEU* 3.3 26.1 - - + +
157A LYS* 3.5 34.5 - - + -
158A VAL* 3.8 7.6 - - + +
161A LEU* 3.1 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 2.8 16.3 + - - +
115A THR* 3.4 13.5 - - + +
117A ALA* 1.3 70.3 - - - +
119A LEU* 1.3 66.3 + - - +
121A SER* 2.3 28.2 + - - +
122A TYR* 3.2 25.8 + - + +
161A LEU* 4.2 11.8 - - + +
165A TYR* 3.7 15.7 - - - +
180A ASN* 3.1 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 3.7 26.7 - - + -
111A CYS* 4.6 2.9 - - - -
115A THR* 2.9 37.1 + - + +
116A LEU* 4.0 2.9 - - - +
118A LEU* 1.3 80.0 - - + +
120A GLY* 1.3 64.1 + - - +
122A TYR* 3.3 5.5 + - - -
123A THR* 3.0 24.4 + - - -
177A PHE* 3.2 61.2 - - + +
180A ASN* 3.7 18.8 - - + -
181A ALA* 3.9 6.7 - - + +
184A LEU* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU 2.7 23.9 + - - -
117A ALA 3.9 1.6 - - - -
119A LEU* 1.3 72.1 - - - +
121A SER* 1.3 57.4 + - - +
123A THR* 2.9 22.4 + - - -
124A ILE* 2.9 15.0 + - - +
146A LEU* 4.2 24.0 - - - +
158A VAL* 3.6 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA 3.1 9.2 + - - -
118A LEU* 2.3 25.3 + - - +
120A GLY* 1.3 74.1 - - - +
122A TYR* 1.3 65.0 + - - +
124A ILE* 3.0 14.7 + - - +
125A GLN* 3.0 12.6 + - - +
158A VAL* 3.3 19.2 - - - +
161A LEU* 3.3 30.4 - - - +
162A HIS* 4.1 3.0 + - - +
165A TYR* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.2 38.5 + - + +
119A LEU* 3.3 7.2 + - - +
121A SER* 1.3 81.6 + - - +
123A THR* 1.3 62.3 + - - +
125A GLN* 3.4 3.3 + - - -
126A SER* 3.0 28.5 + - - -
165A TYR* 3.7 32.8 + + - -
168A MET* 3.8 19.1 - - + -
173A ALA* 3.5 21.1 - - - +
176A GLU* 3.3 40.5 + - + +
177A PHE* 3.7 23.6 - - + -
180A ASN* 3.6 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.5 45.7 + - - +
119A LEU 3.0 13.4 + - - -
120A GLY* 2.9 13.7 + - - -
122A TYR* 1.3 76.5 - - - +
124A ILE* 1.3 61.1 + - + +
126A SER* 3.5 6.9 + - - -
127A GLU* 3.0 31.5 + - + +
144A PHE* 4.8 1.6 - - + -
146A LEU* 4.0 19.0 - - + +
174A ASP* 6.0 0.2 - - - -
177A PHE* 3.4 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY 2.9 13.9 + - - +
121A SER* 3.0 7.8 + - - +
123A THR* 1.3 77.3 - - - +
125A GLN* 1.3 59.9 + - - +
127A GLU* 4.8 1.1 - - - -
128A LEU* 2.8 58.5 + - + +
140A TYR* 4.0 5.2 - - + -
141A VAL* 3.9 16.6 - - + -
144A PHE* 3.7 38.1 - - + -
146A LEU* 4.2 6.7 - - + -
158A VAL* 3.6 19.3 - - + -
162A HIS* 3.5 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER 3.0 7.1 + - - +
122A TYR* 3.5 9.9 - - - +
124A ILE* 1.3 74.8 - - - +
126A SER* 1.3 64.6 + - - +
129A GLY* 2.5 39.2 + - - -
130A ASP* 3.5 21.8 + - - +
162A HIS* 3.0 32.2 + - - +
165A TYR* 3.5 44.2 + - + +
168A MET* 3.0 38.5 - - + +
170A PRO* 5.7 1.4 - - - +
173A ALA* 3.6 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 5.9 6.7 - - - -
101A ARG* 6.2 0.9 - - - -
122A TYR 3.0 13.5 + - - -
123A THR* 3.6 10.4 - - - -
125A GLN* 1.3 79.4 - - - +
127A GLU* 1.3 65.8 + - - +
128A LEU 5.0 0.3 - - - -
129A GLY* 4.7 0.7 + - - -
170A PRO* 3.8 28.2 + - - +
173A ALA* 3.2 15.1 - - - +
174A ASP* 3.0 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.7 24.4 + - - -
98A LEU* 5.1 0.9 - - - +
101A ARG* 3.7 25.8 + - - +
123A THR* 3.0 20.1 + - + +
124A ILE 4.3 1.3 - - - +
126A SER* 1.3 80.0 - - - +
128A LEU* 1.3 64.4 + - - +
144A PHE* 3.7 37.0 - - + -
1B MET* 3.8 17.2 - - - +
63B LYS* 2.9 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 2.8 45.4 + - + +
125A GLN 3.0 0.6 + - - -
126A SER 5.0 0.2 - - - -
127A GLU* 1.3 80.2 - - - +
129A GLY* 1.3 63.7 + - - +
130A ASP 4.8 0.7 - - - +
135A LEU* 3.9 22.4 - - + +
140A TYR* 3.6 27.4 - - + -
144A PHE* 4.1 29.6 - - + -
1B MET* 3.4 28.5 - - - +
2B HIS 5.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN* 2.5 30.6 + - - -
126A SER 4.7 0.2 + - - -
128A LEU* 1.3 76.6 - - - +
130A ASP* 1.3 71.3 + - - +
135A LEU* 4.1 0.2 - - - +
162A HIS* 3.1 16.3 + - - -
168A MET 5.7 1.1 - - - -
170A PRO* 6.5 0.9 - - - -
1B MET* 5.4 1.6 - - - -
----------------------------------------------------------
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