Contacts of the helix formed by residues 134 - 141 (chain C) in PDB entry 3HB8
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 VAL 134 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TRP* 4.9 6.5 - - + -
95C SER 5.0 0.2 - - - +
96C THR* 4.2 14.9 - - + +
109C TRP* 4.2 23.6 - - + -
131C LEU* 4.0 39.3 - - + +
132C GLY 2.6 18.2 + - - +
133C PRO* 1.3 76.1 - - - +
135C TYR* 1.3 74.0 + - + +
136C GLY 3.3 2.9 - - - +
137C PHE 2.9 13.9 + - - -
138C GLN* 3.1 9.0 + - - -
190C MET* 4.3 17.7 - - + -
192C LEU* 4.3 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 3.4 32.1 - + + -
109C TRP* 3.8 34.3 - + - -
134C VAL* 1.3 76.8 - - + +
136C GLY* 1.3 64.6 + - - +
138C GLN* 3.1 7.9 + - - +
139C TRP* 2.8 42.7 + + - +
181C ALA* 4.1 13.9 - - + -
192C LEU* 5.5 2.7 - - + -
194C PRO* 3.5 26.5 - - + +
195C CYS* 2.8 27.9 + - - +
196C HIS* 3.0 47.2 + + + -
230C TYR* 4.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TRP* 6.1 0.4 - - - -
91C PHE* 3.7 20.0 - - - -
94C GLY* 3.5 25.7 - - - -
95C SER 4.0 9.7 + - - -
134C VAL* 3.1 4.6 + - - +
135C TYR* 1.3 77.1 - - - +
137C PHE* 1.3 64.4 + - - +
139C TRP* 3.4 1.6 + - - +
140C ARG* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLY 3.7 4.9 + - - -
96C THR* 3.5 23.2 - - + +
133C PRO* 3.3 24.9 - - + -
134C VAL 2.9 9.4 + - - +
136C GLY* 1.3 73.5 - - - +
138C GLN* 1.3 63.1 + - - +
141C HIS* 2.7 62.6 + + + -
143C GLY 5.3 0.2 - - - -
144C ALA* 3.4 42.0 - - + -
146C TYR* 3.6 32.1 - + + -
153C TYR* 3.5 38.4 - + - -
186C ASP* 4.1 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C PRO* 2.9 30.0 - - - +
134C VAL 3.1 6.8 + - - +
135C TYR* 3.6 7.4 - - - +
137C PHE* 1.3 80.4 - - - +
139C TRP* 1.3 56.8 + - - +
140C ARG 3.5 0.2 + - - -
142C PHE* 3.4 46.4 + - - +
143C GLY 4.4 0.6 - - - +
160C GLN* 2.6 27.4 + - - -
180C CYS 4.5 0.2 - - - +
181C ALA* 3.9 36.1 - - + +
183C ASN* 4.0 11.5 - - - +
186C ASP* 2.8 27.1 + - - +
190C MET* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.7 26.5 - - + -
91C PHE* 3.5 42.8 - + + +
92C ILE* 4.5 6.5 - - + -
135C TYR* 2.8 39.6 + + + +
136C GLY* 3.7 4.9 - - - +
138C GLN* 1.3 76.1 - - - +
140C ARG* 1.3 66.3 + - - +
159C ASP* 3.7 1.0 - - - +
160C GLN* 3.0 29.3 + - - +
161C LEU* 3.2 25.7 + - + -
179C MET* 3.5 44.6 - - + +
181C ALA* 4.5 14.8 - - + +
230C TYR* 3.7 27.3 + + - -
233C LEU* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE 4.4 0.9 - - - +
92C ILE* 2.9 36.4 + - - +
93C LYS 4.9 0.7 - - - -
94C GLY* 3.9 9.6 - - - -
136C GLY 3.3 14.3 + - - +
139C TRP* 1.3 89.0 - - - +
141C HIS* 1.3 88.9 + - + +
156C GLN 4.2 1.6 - - - +
157C GLY 4.8 0.2 - - - +
158C VAL 3.4 6.6 - - - +
159C ASP* 2.9 57.8 + - - +
161C LEU* 3.5 27.5 - - - +
162C GLN* 4.3 13.3 + - - +
288C ILE* 4.3 1.0 - - - +
289C ASP* 3.1 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LYS 5.9 0.2 + - - -
94C GLY* 5.3 7.6 + - - -
136C GLY 5.0 0.2 - - - -
137C PHE* 2.7 50.8 + + + +
140C ARG* 1.3 102.8 + - + +
142C PHE* 1.3 64.9 + - - +
143C GLY 3.3 0.5 + - - -
144C ALA* 3.1 22.8 + - + +
153C TYR* 2.9 47.4 + + + +
154C SER* 4.9 2.5 - - - -
155C GLY 5.3 0.8 + - - -
156C GLN 3.2 17.2 + - - +
157C GLY* 3.8 1.3 - - - -
158C VAL 3.7 3.1 - - - +
159C ASP* 5.7 0.7 - - - -
----------------------------------------------------------
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