Contacts of the helix formed by residues 141 - 151 (chain B) in PDB entry 3GHG
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 GLU 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN* 4.1 27.8 + - - +
138B VAL 4.2 5.1 + - - +
139B VAL 4.0 3.0 + - - -
140B ASN* 1.3 92.3 + - - +
142B TYR* 1.3 63.2 + - - +
143B SER* 3.4 1.3 + - - -
144B SER* 2.5 49.0 + - - +
145B GLU* 3.0 16.3 + - + +
77C ASN* 5.0 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 5.2 12.4 - + - -
116A ARG* 4.1 37.8 + - - -
200A GLN 5.1 10.1 - - - +
139B VAL 4.2 19.5 - - - -
140B ASN* 5.6 1.1 - - - -
141B GLU* 1.3 75.4 - - - +
143B SER* 1.3 78.4 + - - +
145B GLU* 3.2 7.4 + - - +
146B LEU* 2.7 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 3.8 19.5 + - - -
140B ASN* 3.4 16.6 + - - -
141B GLU 3.4 0.2 - - - -
142B TYR* 1.3 92.3 - - - +
144B SER* 1.3 64.5 + - - +
146B LEU* 3.3 15.7 + - - +
147B GLU* 3.5 12.0 + - - +
82C ALA* 4.7 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU* 2.5 56.2 + - - +
143B SER* 1.3 79.1 + - - +
145B GLU* 1.3 60.6 + - - -
147B GLU* 3.3 19.1 + - - +
148B LYS* 3.8 20.6 + - - +
77C ASN* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 3.4 33.7 + - - +
199A ARG 5.2 2.9 - - - +
200A GLN* 4.9 1.6 - - - +
141B GLU* 3.0 17.9 + - + +
142B TYR* 3.6 7.8 - - - +
144B SER* 1.3 76.8 - - - +
146B LEU* 1.3 79.7 + - - +
147B GLU 3.3 0.6 + - - -
148B LYS* 4.0 10.9 + - - +
149B HIS* 3.4 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 5.1 14.8 - - + -
119A ILE* 6.6 0.2 - - + -
200A GLN* 3.2 51.8 - - + +
142B TYR* 2.7 39.7 + - + +
143B SER* 3.7 10.1 - - - +
144B SER 3.2 0.8 - - - -
145B GLU* 1.3 96.5 - - - +
147B GLU* 1.3 56.9 + - - +
149B HIS* 3.6 14.5 + - + +
150B GLN* 3.5 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER 3.5 7.1 + - - +
144B SER* 3.3 13.1 + - - +
146B LEU* 1.3 76.4 - - - +
148B LYS* 1.3 68.9 + - + +
149B HIS 3.2 1.3 - - - -
150B GLN* 3.4 14.4 + - + +
151B LEU* 3.5 18.3 + - + +
85C LYS* 3.8 27.5 + - - +
89C MET* 3.1 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 5.8 1.0 - - - -
144B SER* 3.8 23.9 + - - +
145B GLU* 4.0 9.1 + - - +
147B GLU* 1.3 79.2 - - + +
149B HIS* 1.3 64.2 + - - +
150B GLN 3.4 0.2 - - - -
151B LEU* 3.5 31.4 + - + +
152B TYR* 4.1 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 5.5 7.4 - - + +
123A LYS* 3.2 33.1 + - - -
197A ARG* 3.3 41.7 + - + +
200A GLN* 2.6 46.9 + - + +
145B GLU* 3.4 20.4 + - - +
146B LEU* 3.6 16.2 + - + +
147B GLU 3.2 0.2 - - - -
148B LYS* 1.3 77.4 - - - +
150B GLN* 1.3 69.7 + - - +
151B LEU 3.4 0.3 + - - -
152B TYR* 3.4 21.0 + - + +
153B ILE* 4.2 5.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.2 38.8 - - + +
146B LEU 3.5 12.6 + - - +
147B GLU* 3.4 13.1 + - - +
148B LYS 3.4 0.4 - - - -
149B HIS* 1.3 83.7 + - - +
151B LEU* 1.3 55.6 + - + +
152B TYR 3.0 0.2 - - - -
153B ILE* 2.4 38.0 + - + +
154B ASP* 3.0 24.4 + - + +
89C MET* 4.4 28.5 + - - +
92C GLU* 4.8 8.0 - - - +
93C ILE* 4.7 3.6 - - - +
96C TYR* 4.3 12.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLU* 3.6 13.5 - - + +
148B LYS* 3.5 30.9 + - + +
149B HIS 3.2 1.2 - - - -
150B GLN* 1.3 77.1 - - + +
152B TYR* 1.3 59.3 + - - +
154B ASP* 4.0 14.8 - - + +
155B GLU* 3.4 48.6 + - + +
----------------------------------------------------------
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