Contacts of the helix formed by residues 140 - 149 (chain A) in PDB entry 3GBA
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 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.3 2.7 - - - -
62A GLY 4.6 1.1 - - - -
95A ARG* 4.2 4.7 - - - -
137A VAL 4.0 3.9 + - - -
138A ARG 3.3 4.9 + - - -
139A ASP* 1.3 80.5 - - - +
141A SER* 1.3 63.1 + - - -
142A THR 3.3 2.9 + - - -
143A MET* 3.4 3.6 + - - +
144A THR* 3.1 27.8 + - - -
258A DYH 3.3 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.3 25.9 + - - +
92A THR* 4.2 15.7 - - - -
95A ARG* 3.9 6.7 - - - +
140A GLY* 1.3 69.6 - - - -
142A THR* 1.3 60.9 + - - +
144A THR* 3.7 7.5 - - - -
145A PHE* 2.9 28.8 + - - +
190A GLU* 3.3 6.2 + - - -
214A LYS* 4.3 7.7 + - - -
258A DYH 2.8 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.7 31.7 - - + +
136A ALA* 4.0 9.4 - - + -
137A VAL 5.7 0.2 - - - -
141A SER* 1.3 74.7 + - - +
143A MET* 1.3 66.7 + - - +
145A PHE* 3.2 2.9 + - - +
146A PHE* 3.2 26.6 + - + -
188A LEU* 3.7 40.6 - - + +
189A MET* 4.4 1.7 - - - -
190A GLU* 4.0 6.6 + - - +
214A LYS* 5.0 0.3 + - - -
258A DYH 2.7 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA* 3.7 22.7 - - + -
136A ALA* 4.3 11.4 - - + +
137A VAL 3.6 19.6 + - - +
138A ARG* 4.9 1.1 - - - -
139A ASP* 3.7 22.2 - - - +
140A GLY 3.4 5.7 + - - +
142A THR* 1.3 78.7 - - - +
144A THR* 1.3 78.6 + - - +
146A PHE* 3.2 6.2 + - - +
147A LYS* 2.9 51.1 + - + +
158A TRP* 3.9 23.9 - - + -
161A MET* 5.7 0.2 - - - -
169A LEU* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY 5.1 0.9 + - - -
63A ALA* 4.1 10.0 - - - +
70A TRP* 6.5 0.2 - - + -
94A VAL* 4.9 8.5 - - + -
140A GLY 3.1 17.1 + - - -
141A SER* 3.7 8.2 - - - -
142A THR 3.2 0.4 - - - -
143A MET* 1.3 92.1 - - - +
145A PHE* 1.3 67.0 + - - +
147A LYS* 3.3 4.2 + - + +
148A LYS* 3.0 59.9 + - + +
260A GOL 5.7 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.6 17.9 - - + -
141A SER 2.9 14.8 + - - +
142A THR 3.4 8.7 - - - +
144A THR* 1.3 76.6 - - - +
146A PHE* 1.3 73.8 + + - +
148A LYS* 3.8 2.2 - - - +
149A SER* 3.1 28.6 + - - -
151A ILE* 5.5 2.9 - - + -
154A TYR* 3.8 34.1 - + + -
211A ILE* 3.8 32.8 - - + -
212A ASP* 3.7 29.8 - - + -
214A LYS* 4.9 1.6 - - - +
260A GOL 5.3 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 4.3 1.3 - - + -
142A THR* 3.2 28.8 + - + -
143A MET 3.2 7.1 + - - +
145A PHE* 1.3 88.5 - + - +
147A LYS* 1.3 67.6 + - - +
148A LYS 3.2 1.0 + - - -
149A SER* 3.4 14.8 + - - +
154A TYR* 3.7 41.6 - + + +
155A GLU* 5.1 0.7 - - - -
157A MET* 3.8 21.3 - - + -
158A TRP* 3.4 31.1 - - + +
161A MET* 3.8 20.2 - - + -
188A LEU* 3.5 41.7 - - + -
211A ILE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN 4.8 11.3 + - - -
65A ASN* 6.0 2.4 - - - +
143A MET* 2.9 34.7 + - + +
144A THR* 3.7 7.4 - - + +
146A PHE* 1.3 75.7 - - - +
148A LYS* 1.3 66.3 + - + +
149A SER 4.9 1.2 - - - +
150A LYS* 5.2 1.9 + - - -
158A TRP* 3.6 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 5.6 5.1 + - - +
70A TRP* 6.0 0.6 - - - -
94A VAL* 3.1 43.9 - - + +
144A THR* 3.0 37.1 + - + +
145A PHE* 3.8 2.2 - - - +
147A LYS* 1.3 86.7 - - + +
149A SER* 1.3 65.5 + - - +
150A LYS* 3.2 22.3 + - - +
260A GOL 5.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 3.1 23.8 + - - -
146A PHE 3.4 9.3 + - - +
147A LYS 4.9 1.6 - - - +
148A LYS* 1.3 79.5 - - - +
150A LYS* 1.3 66.3 + - - +
151A ILE* 3.1 20.8 + - - +
154A TYR* 3.5 34.9 - - - +
155A GLU* 3.2 18.4 - - - +
----------------------------------------------------------
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