Contacts of the helix formed by residues 134 - 142 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 4.9 5.2 - - + -
95A SER 4.5 2.7 - - - +
96A THR* 3.8 17.3 - - + -
109A TRP* 4.0 24.2 - - + -
131A LEU* 3.6 43.1 - - + +
132A GLY 2.8 17.5 + - - +
133A PRO* 1.3 76.1 - - - +
135A TYR* 1.3 72.1 + - + +
136A GLY 4.4 4.3 - - - +
137A PHE* 2.9 14.4 + - - +
138A GLN* 3.1 6.4 + - - -
190A MET* 4.6 17.5 - - + -
191A ALA* 4.8 2.9 - - + +
192A LEU* 5.1 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 5.9 0.2 - - - -
91A PHE* 3.4 43.5 - + + -
109A TRP* 3.8 26.0 - + - -
134A VAL* 1.3 75.0 - - + +
136A GLY* 1.3 65.8 + - - +
138A GLN* 3.2 4.8 + - - +
139A TRP* 2.9 40.6 + + - +
181A ALA* 3.9 14.4 - - + -
192A LEU* 5.9 2.4 - - + +
194A PRO* 3.3 25.4 - - + +
195A CYS* 2.6 30.8 + - - +
196A HIS* 3.1 40.8 - + + -
230A TYR* 4.9 3.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
91A PHE* 3.5 33.1 - - - -
94A GLY* 3.8 17.4 - - - -
95A SER 4.2 4.9 + - - -
134A VAL* 3.1 6.1 + - - +
135A TYR* 1.3 77.9 - - - +
137A PHE* 1.3 64.3 + - - +
139A TRP* 3.0 11.3 + - - +
140A ARG* 3.2 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY 3.9 9.0 + - - -
96A THR* 3.7 12.7 - - + +
133A PRO* 3.3 34.1 - - + -
134A VAL 2.9 13.8 + - - +
136A GLY* 1.3 69.6 - - - +
138A GLN* 1.3 62.2 + - - +
141A HIS* 2.7 63.7 + + + +
143A GLY 5.3 0.4 - - - -
144A ALA* 3.6 34.3 - - + -
146A TYR* 3.6 23.6 - + + -
153A TYR* 3.4 40.2 - + - -
186A ASP* 3.6 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO* 3.0 26.9 + - - +
134A VAL 3.1 6.3 + - - +
135A TYR 3.8 5.6 - - - +
137A PHE* 1.3 82.1 - - - +
139A TRP* 1.3 57.7 + - - +
140A ARG 3.6 0.2 + - - -
142A PHE* 3.0 42.5 - - + +
160A GLN* 2.8 26.2 + - - -
181A ALA* 3.6 36.3 - - + +
183A ASN* 3.1 17.1 + - - +
186A ASP* 2.7 38.4 + - - +
190A MET* 4.4 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.8 27.1 - - + -
91A PHE* 3.5 44.9 - + + -
92A ILE* 4.5 8.1 - - + -
135A TYR* 2.9 36.6 + + + +
136A GLY* 3.0 10.1 + - - +
138A GLN* 1.3 80.9 - - - +
140A ARG* 1.3 66.1 + - + +
160A GLN* 2.9 29.6 + - - +
161A LEU* 3.2 25.0 + - + -
179A MET* 3.4 44.6 + - + +
181A ALA* 4.4 15.0 - - + +
230A TYR* 3.6 26.0 + + - -
233A LEU* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE 4.4 1.3 - - - +
92A ILE* 2.6 53.5 + - - +
93A LYS* 4.8 1.3 - - - +
94A GLY* 4.4 6.7 - - - +
136A GLY 3.2 10.5 + - - +
137A PHE 3.2 2.8 + - - -
139A TRP* 1.3 85.9 - - + +
141A HIS* 1.3 90.4 + - + +
156A GLN 4.0 1.0 - - - +
158A VAL 3.0 11.3 - - - +
159A ASP* 3.1 46.0 + - - +
161A LEU* 3.8 15.4 - - + +
162A GLN* 4.2 11.7 + - - +
288A ILE* 4.0 12.7 - - - +
289A ASP* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS 5.9 0.2 + - - -
94A GLY* 5.3 9.5 - - - -
136A GLY 5.3 0.2 - - - -
137A PHE* 2.7 50.9 + + + +
140A ARG* 1.3 102.4 + - + +
142A PHE* 1.3 67.4 + - - +
143A GLY 3.3 0.3 + - - -
144A ALA* 3.0 21.0 + - + +
153A TYR* 3.2 40.9 + + + +
154A SER* 4.1 6.7 - - - -
155A GLY 5.0 0.9 - - - -
156A GLN 3.1 23.5 + - - +
157A GLY* 3.9 0.9 - - - -
158A VAL 3.4 3.6 - - - -
159A ASP* 5.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLN* 3.0 39.9 + - - +
141A HIS* 1.3 75.4 - - - +
143A GLY* 1.3 65.7 + - - +
157A GLY* 3.1 5.9 - - - -
158A VAL* 2.9 40.6 + - + +
160A GLN* 3.5 23.1 - - - +
180A CYS* 3.6 14.8 - - + -
182A TRP 4.0 14.8 - - - -
183A ASN* 3.9 25.1 - - + -
185A ARG* 6.4 0.4 - - - -
142B PHE* 4.4 7.4 - + - -
182B TRP 4.7 1.3 - - - -
183B ASN* 3.5 16.8 - - - -
184B PRO* 3.4 36.8 - - + -
185B ARG* 4.3 5.2 - - - +
----------------------------------------------------------
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