Contacts of the helix formed by residues 137 - 151 (chain A) in PDB entry 4GAB
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 THR 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.6 10.7 - - - +
113A PRO 5.7 0.2 - - - -
115A GLY* 5.8 1.6 - - - +
135A LYS 4.6 6.1 - - - +
136A ALA* 1.3 77.3 - - - +
138A PHE* 1.3 62.2 + - - +
139A LEU* 3.2 22.8 + - - +
140A ASP* 3.0 24.6 + - - +
141A ALA 3.0 22.7 + - - -
309A ASP* 5.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.8 16.4 - - + -
110A ILE* 3.4 20.4 - - + +
113A PRO* 3.4 37.5 + - + +
137A THR* 1.3 76.9 - - - +
139A LEU* 1.3 78.7 + - + +
141A ALA* 3.7 3.1 - - - -
142A TRP* 2.9 28.6 + - - +
162A PHE* 3.6 30.5 - + + -
166A GLN* 3.8 23.3 - - + -
169A LYS* 3.8 22.0 - - + -
170A LEU* 4.3 8.1 - - + -
309A ASP* 3.7 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR* 3.1 10.2 + - - +
138A PHE* 1.3 104.6 - - + +
140A ASP* 1.3 65.5 + - - +
142A TRP* 3.4 4.8 + - - +
143A GLU* 3.2 29.8 + - - +
169A LYS* 3.9 28.0 - - + +
170A LEU* 4.0 22.0 - - + -
173A LYS* 4.0 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 4.2 4.3 - - - +
86A ARG* 5.1 4.6 + - - +
135A LYS 4.6 1.0 - - - +
136A ALA* 3.5 17.8 - - + -
137A THR* 3.0 36.0 + - - +
139A LEU* 1.3 79.5 - - - +
141A ALA* 1.3 63.4 + - - +
143A GLU* 3.3 24.3 + - - +
144A ALA* 3.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.9 14.4 - - + -
84A PHE* 3.5 49.1 + - + +
89A VAL* 4.2 4.7 - - - +
110A ILE* 4.4 4.3 - - + -
137A THR 3.0 6.6 + - - +
138A PHE* 3.6 8.5 - - - +
140A ASP* 1.3 76.1 - - - +
142A TRP* 1.3 62.5 + - - +
144A ALA* 3.1 5.9 + - - +
145A MET* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.7 21.3 - - + +
138A PHE 2.9 17.1 + - - +
139A LEU* 3.6 7.2 - - - +
141A ALA* 1.3 75.8 - - - +
143A GLU* 1.3 58.5 + - - +
145A MET* 3.1 9.0 + - + +
146A GLU* 2.9 62.9 + - - +
157A LEU* 3.3 37.7 - - + -
158A GLY 3.4 21.3 - - - -
159A VAL* 3.7 10.3 - - + -
170A LEU* 3.6 29.4 - - + -
173A LYS* 4.6 4.9 - - + -
176A LEU* 3.4 8.5 - - + +
178A TYR 2.9 28.7 + - - -
179A LYS 3.9 0.4 - - - -
180A PRO* 3.7 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 3.7 24.9 + - - +
139A LEU* 3.2 15.5 + - - +
140A ASP* 3.6 15.3 - - - +
141A ALA 3.2 0.2 - - - -
142A TRP* 1.3 76.4 - - - +
144A ALA* 1.3 61.9 + - - +
146A GLU* 3.5 21.3 + - - +
147A GLU* 3.6 15.6 + - - +
173A LYS* 2.7 40.2 + - - +
177A LYS* 5.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 3.7 31.1 - - + +
89A VAL* 3.7 28.2 - - + +
90A ARG* 4.8 1.2 + - - -
140A ASP 3.4 6.0 + - - +
141A ALA 3.1 8.7 + - - +
143A GLU* 1.3 76.3 - - - +
145A MET* 1.3 65.7 + - - +
147A GLU* 3.3 28.6 + - - +
148A LEU* 3.8 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.9 12.1 - - - -
89A VAL* 3.9 14.8 - - + -
108A TYR* 3.5 45.3 - - + +
109A LEU 3.8 3.8 - - - +
110A ILE* 3.5 44.0 - - + +
141A ALA 2.9 19.2 + - - +
142A TRP* 3.1 12.8 + - + +
144A ALA* 1.3 76.1 - - - +
146A GLU* 1.3 63.2 + - - +
148A LEU* 3.0 28.3 + - + +
149A VAL 3.5 3.3 + - - -
157A LEU* 3.7 24.2 - - + +
158A GLY 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TRP* 2.9 44.9 + - + +
143A GLU* 3.7 22.6 - - - +
144A ALA 3.3 0.4 - - - -
145A MET* 1.3 76.6 - - - +
147A GLU* 1.3 63.1 + - - +
149A VAL 3.1 3.2 + - - +
150A ASP* 3.0 21.4 + - - -
157A LEU* 3.9 8.1 - - + -
173A LYS* 4.6 3.5 + - - -
175A GLY 4.7 1.4 - - - +
176A LEU* 3.6 3.4 - - - +
177A LYS* 2.8 52.2 + - + +
178A TYR* 3.0 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 2.2 43.3 + - - +
90A ARG* 3.8 19.5 + - - +
143A GLU 3.6 11.2 - - - +
144A ALA* 3.3 12.9 + - - +
145A MET 3.1 0.4 - - - -
146A GLU* 1.3 76.8 - - - +
148A LEU* 1.3 56.9 + - - +
150A ASP* 3.4 10.0 + - - +
151A GLU* 3.0 42.1 + - - +
177A LYS* 4.5 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.8 4.5 - - + -
90A ARG* 3.4 39.9 - - - +
93A PHE* 3.7 48.7 - - + -
108A TYR* 3.8 21.8 - - + -
144A ALA 3.9 6.7 - - - +
145A MET* 3.0 21.9 + - + +
147A GLU* 1.3 78.3 - - - +
149A VAL* 1.3 57.9 + - - +
151A GLU* 3.5 2.9 + - - -
152A GLY 3.3 3.3 + - - -
153A LEU* 2.9 33.8 + - + +
154A VAL* 3.3 17.9 + - + -
157A LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET 4.0 2.9 - - - +
146A GLU 3.1 7.7 + - - +
148A LEU* 1.3 74.3 - - - +
150A ASP* 1.3 65.4 + - - +
151A GLU 3.1 0.4 - - - -
152A GLY* 3.1 13.9 + - - -
154A VAL* 3.4 26.2 - - + +
155A LYS* 4.0 13.0 - - - +
156A ALA* 4.6 4.5 - - - -
157A LEU* 3.7 39.0 - - + +
178A TYR* 3.5 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU 3.0 13.0 + - - +
147A GLU* 3.6 11.9 - - - +
149A VAL* 1.3 76.8 - - - +
151A GLU* 1.3 63.1 + - + +
152A GLY 3.5 0.5 + - - -
177A LYS* 3.0 32.9 + - - +
178A TYR* 2.6 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 2.9 41.6 + - - -
147A GLU* 3.0 23.2 + - - +
148A LEU 3.5 3.8 + - - +
149A VAL 3.1 0.4 - - - -
150A ASP* 1.3 81.1 - - + +
152A GLY* 1.3 60.7 + - - +
153A LEU* 3.4 17.6 + - + +
----------------------------------------------------------
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