Contacts of the helix formed by residues 126 - 134 (chain H) in PDB entry 2AAZ
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 126 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H TRP* 4.7 6.7 - - + -
87H CYS 5.3 0.4 - - - +
88H THR* 3.9 17.6 - - + +
101H TRP* 6.3 5.2 - - + -
123H LEU* 3.7 44.2 - - + +
124H GLY 2.8 16.1 + - - +
125H PRO* 1.3 75.6 - - - +
127H TYR* 1.3 81.9 + - + +
128H GLY 5.0 1.3 - - - +
129H PHE 2.8 15.6 + - - -
130H GLN* 3.3 7.2 + - - -
182H MET* 3.8 25.6 - - + -
183H ALA 4.5 1.6 - - - +
184H LEU* 4.0 13.2 - - + +
186H PRO* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H TRP* 5.3 0.2 - + - -
83H PHE* 3.4 34.3 - + + -
101H TRP* 3.7 29.6 - + - -
126H VAL* 1.3 86.1 - - + +
128H GLY* 1.3 66.5 + - - +
130H GLN* 3.0 2.8 + - - +
131H TRP* 3.0 32.5 + - - +
173H ALA* 3.9 22.8 - - + +
184H LEU 5.8 2.2 - - - -
185H PRO 4.3 1.1 + - - -
186H PRO* 3.5 19.9 - - + +
187H CYS* 2.7 28.9 + - - +
188H HIS* 3.2 53.3 - + + -
700H UMP 3.7 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H TRP* 6.2 0.2 - - - -
83H PHE* 3.1 34.2 - - - -
86H GLY* 3.2 21.8 - - - -
87H CYS 4.6 5.3 + - - -
126H VAL* 3.1 3.6 + - - +
127H TYR* 1.3 78.8 - - - +
129H PHE* 1.3 62.6 + - - +
131H TRP* 3.4 5.9 + - - +
132H ARG* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H GLY 3.6 11.2 + - - +
88H THR* 3.6 18.6 - - + +
125H PRO* 3.4 28.0 - - + -
126H VAL 2.8 15.8 + - - +
128H GLY* 1.3 71.7 - - - -
130H GLN* 1.3 64.5 + - - +
133H HIS* 2.7 54.6 + + + +
135H GLY 5.3 0.4 - - - -
136H ALA* 3.7 37.7 - - + -
138H TYR* 3.6 31.4 - + + -
145H TYR* 3.6 36.1 - + - -
178H ASP* 4.2 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H PRO* 3.0 31.0 + - - +
126H VAL 3.3 5.6 + - - +
127H TYR 3.0 4.7 + - - +
129H PHE* 1.3 80.6 - - - +
131H TRP* 1.3 61.0 + - - +
134H PHE* 3.1 34.7 + - + +
135H GLY 4.4 0.2 + - - -
152H GLN* 2.9 19.9 + - - -
172H SER 4.0 1.8 - - - +
173H ALA* 3.3 38.4 - - - +
175H ASN* 3.0 25.4 + - + +
178H ASP* 2.9 33.3 + - - +
182H MET* 4.1 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU* 4.5 8.7 - - + -
83H PHE* 3.6 45.8 - + + -
84H VAL* 4.4 11.4 - - + -
127H TYR* 3.0 26.1 + - + +
128H GLY* 3.6 6.3 - - - +
130H GLN* 1.3 77.6 - - - +
132H ARG* 1.3 65.8 + - - +
152H GLN* 3.0 29.7 + - - +
153H LEU* 3.4 16.1 + - + -
171H LEU* 3.8 40.1 + - + +
172H SER 4.0 6.9 - - - +
173H ALA* 3.8 25.1 - - + +
188H HIS* 4.4 9.7 + + - -
190H PHE* 6.3 0.2 - - - +
230H SER* 6.1 0.2 - - - -
231H TYR* 3.4 27.0 + + - -
234H LEU* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H PHE 4.5 0.2 - - - +
84H VAL* 2.8 37.8 + - - +
85H SER* 4.6 1.9 - - - +
86H GLY* 4.0 6.5 - - - +
128H GLY 3.2 15.8 + - - +
131H TRP* 1.3 81.1 - - + +
133H HIS* 1.3 87.2 + - + +
148H LYS 4.0 1.4 - - - +
149H GLY 4.7 0.5 - - - +
150H VAL 3.3 7.1 - - - -
151H ASP* 2.8 58.2 + - - +
153H LEU* 3.6 32.5 - - - +
154H GLN* 4.4 8.3 - - - +
292H ILE* 4.3 5.9 - - - +
293H ASP* 2.7 42.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 133 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H SER 5.2 2.4 + - - -
86H GLY* 4.7 10.8 - - - -
129H PHE* 2.7 45.3 + + + +
132H ARG* 1.3 97.3 + - + +
134H PHE* 1.3 66.9 + - - +
135H GLY 3.1 0.2 + - - -
136H ALA* 2.9 26.3 + - + +
145H TYR* 3.0 39.5 + + + +
146H LYS* 4.2 6.7 - - - -
147H GLY 4.6 3.1 + - - -
148H LYS 2.9 26.1 + - - +
149H GLY* 3.8 0.7 - - - -
150H VAL 3.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G PHE* 3.9 16.8 - + - -
175G ASN* 3.6 15.7 - - - -
176G PRO* 3.4 42.6 - - + -
177G LYS* 4.0 8.5 - - + +
130H GLN* 3.1 40.6 + - - +
133H HIS* 1.3 75.1 - - - +
135H GLY* 1.3 65.3 + - - +
149H GLY* 3.3 2.8 - - - -
150H VAL* 2.8 39.3 + - + +
152H GLN* 3.6 20.6 - - - +
172H SER* 4.3 6.3 - - - -
174H TRP 3.4 21.3 - - - -
175H ASN* 3.5 20.9 - - - -
----------------------------------------------------------
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