Contacts of the helix formed by residues 135 - 142 (chain A) in PDB entry 3Q2U
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 CYS 135 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 3.1 15.9 - - + +
123A ASP* 3.4 30.1 - - - -
124A TYR* 3.8 24.5 - - + -
131A CYS* 2.1 51.6 - - + -
134A VAL* 1.3 78.3 - - - +
136A GLY* 1.3 59.5 + - - +
137A HIS 3.3 0.7 + - - -
138A TYR* 3.3 5.4 + - + +
139A THR* 3.1 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 3.8 1.9 - - - +
120A GLU* 3.5 0.4 + - - -
134A VAL* 3.8 0.6 - - - +
135A CYS* 1.3 78.9 - - - +
137A HIS* 1.4 59.9 + - - +
139A THR* 3.3 14.4 + - - -
140A GLN* 3.4 9.0 + - - +
180A ASN* 2.8 27.7 + - - -
666A GOL 4.1 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 5.5 8.9 - + - -
99A ASN* 3.2 29.3 + - - +
100A ILE* 3.7 23.1 + - - +
117A TRP* 3.4 41.4 - + + -
120A GLU* 2.6 30.2 + - - +
134A VAL* 3.9 10.6 - - + +
136A GLY* 1.4 72.2 - - - +
138A TYR* 1.3 67.3 + - - +
140A GLN 3.4 1.2 + - - -
141A VAL* 2.9 26.7 + - - +
666A GOL 3.3 31.2 + - - -
898A GOL 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 5.4 2.1 - - + +
49A LYS 5.2 0.9 + - - -
117A TRP 3.3 20.2 + - - +
118A TYR* 3.6 37.2 - + - +
120A GLU* 3.0 14.6 + - + -
121A ILE* 3.7 33.8 - - + +
124A TYR* 3.5 37.7 - + + -
126A PHE* 4.0 21.1 - - - -
135A CYS* 3.5 7.9 - - + +
137A HIS* 1.3 76.7 - - - +
139A THR* 1.3 88.4 + - + +
141A VAL* 3.1 12.4 + - - +
142A VAL* 3.2 33.7 + - + +
185A PRO* 4.5 1.2 - - + +
186A TYR* 4.3 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 3.8 29.8 - - + +
135A CYS* 3.1 16.5 + - + +
136A GLY* 3.3 13.4 + - - -
137A HIS 3.3 0.2 - - - -
138A TYR* 1.3 93.1 - - + +
140A GLN* 1.3 56.5 + - - +
142A VAL* 3.5 7.1 + - - -
143A TRP* 3.0 36.7 + - + -
180A ASN* 2.7 25.9 + - - -
185A PRO* 3.6 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 4.4 1.7 + - - -
97A GLY* 3.5 14.0 - - - -
98A GLU 4.2 4.9 + - - +
99A ASN* 3.8 12.1 - - - +
136A GLY 3.4 14.6 + - - +
137A HIS 3.4 1.0 + - - -
138A TYR 3.2 0.4 - - - -
139A THR* 1.3 77.2 + - - +
141A VAL* 1.4 67.9 + - - +
143A TRP* 3.3 12.1 + - - +
146A SER* 2.9 27.7 + - - -
175A TYR* 3.4 49.1 - - + +
179A GLY* 2.9 26.8 + - - +
180A ASN* 3.7 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 4.0 25.8 - - + +
44A PHE* 4.1 25.6 - - + -
45A ARG* 2.9 26.7 + - - +
58A MET* 4.5 1.0 - - - +
99A ASN* 3.6 13.7 - - - +
114A ILE* 4.5 9.9 - - + -
117A TRP* 3.9 26.5 - - + -
118A TYR* 4.6 7.6 - - + +
137A HIS 2.9 20.6 + - - +
138A TYR* 3.1 10.3 + - - +
140A GLN* 1.4 77.5 - - - +
142A VAL* 1.3 60.9 + - + +
175A TYR* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE 4.5 7.0 - - - +
45A ARG* 3.6 9.4 - - - +
48A VAL* 3.7 28.7 - - + -
55A MET* 3.4 15.1 - - + +
118A TYR* 4.0 23.8 - - + -
138A TYR* 3.2 38.8 + - + +
139A THR* 3.5 6.3 - - - +
141A VAL* 1.3 81.1 - - + +
143A TRP* 1.3 63.8 + - - +
144A ALA 3.1 3.8 + - - -
185A PRO* 3.6 13.8 - - + +
186A TYR* 3.6 10.3 - - + -
----------------------------------------------------------
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