Contacts of the helix formed by residues 118 - 129 (chain B) in PDB entry 1QYR
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 ILE 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 5.2 3.1 - - + -
91B ASP* 4.7 10.8 - - - +
92B ALA* 5.8 2.2 - - + -
93B MET* 3.8 27.4 - - + +
114B LEU* 4.3 5.2 - - + -
115B PRO* 3.5 41.9 - - + +
117B ASN* 1.3 84.8 - - + +
119B SER* 1.3 69.7 + - - +
120B THR 3.4 1.6 - - - -
121B PRO* 3.2 3.7 - - - +
122B LEU* 2.8 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 3.7 14.7 + - - +
115B PRO 3.2 13.5 + - - -
116B TYR 4.0 0.4 - - - -
117B ASN 3.5 1.2 - - - -
118B ILE* 1.3 81.6 - - - +
120B THR* 1.3 62.2 + - - +
122B LEU* 3.3 1.9 + - - +
123B MET* 3.0 29.6 + - - +
140B LEU* 3.6 19.7 - - - +
141B GLN* 2.7 39.6 + - - -
144B VAL* 4.2 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR 5.2 0.8 + - - -
117B ASN 5.1 0.4 + - - -
119B SER* 1.3 76.3 - - - +
121B PRO* 1.3 75.4 - - + +
123B MET* 3.2 18.2 + - - +
124B PHE* 3.4 36.0 + - + -
144B VAL* 3.6 26.7 - - - +
147B ARG* 5.7 3.0 - - - -
160B LEU* 4.1 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B MET* 3.7 33.2 - - + +
117B ASN 4.0 12.8 - - - +
118B ILE 3.2 13.2 - - - +
120B THR* 1.3 98.5 - - + +
122B LEU* 1.3 61.0 + - - +
124B PHE* 3.6 11.1 + - + +
125B HIS* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.7 20.9 - - + -
92B ALA* 3.3 37.5 - - + +
93B MET* 4.0 7.5 - - + +
97B PHE* 4.5 1.1 - - + -
114B LEU* 3.7 28.0 - - + -
118B ILE* 2.8 42.3 + - + +
119B SER 3.8 3.6 - - - +
120B THR 3.2 0.2 - - - -
121B PRO* 1.3 73.6 - - - +
123B MET* 1.3 60.9 + - - +
125B HIS* 3.2 7.7 + - + +
126B LEU* 2.8 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 5.2 1.1 - - + -
119B SER 3.0 19.2 + - - +
120B THR* 3.2 8.3 + - - +
122B LEU* 1.3 74.4 - - - +
124B PHE* 1.3 54.1 + - - +
126B LEU* 3.0 9.0 + - - +
127B PHE* 2.6 56.7 + - + -
136B MET* 5.8 1.3 - - - +
138B PHE* 4.3 21.8 - - - -
140B LEU* 3.5 23.3 - - + -
144B VAL* 4.1 8.3 - - + -
148B LEU* 3.4 43.1 - - + -
160B LEU* 4.7 6.5 - - + -
194B LEU* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 3.4 41.3 + - + -
121B PRO* 3.9 9.4 - - + +
122B LEU 3.4 0.2 - - - -
123B MET* 1.3 78.0 - - - +
125B HIS* 1.3 62.7 + - - +
127B PHE* 3.4 17.2 + + + +
128B SER* 3.1 23.4 + - - -
159B ARG* 3.2 39.9 - - + +
160B LEU* 3.8 33.9 - - + -
163B MET* 3.8 31.4 - - + -
167B TYR* 5.6 1.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ALA 3.3 22.8 + - - -
93B MET* 3.3 23.6 + - + +
94B THR* 4.3 5.8 - - - -
95B PHE 2.6 26.1 + - - -
97B PHE* 4.0 9.6 - + - -
121B PRO 3.1 19.3 + - - +
122B LEU* 3.4 8.1 - - + +
123B MET 3.2 0.2 - - - -
124B PHE* 1.3 75.8 - - - +
126B LEU* 1.3 61.8 + - - +
128B SER* 2.6 28.7 + - - -
129B TYR* 3.2 36.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 4.5 0.9 - - + -
97B PHE* 3.9 39.5 - - + -
110B VAL* 4.4 9.4 - - + -
122B LEU* 2.8 41.3 + - + +
123B MET* 3.5 6.3 - - - +
125B HIS* 1.3 70.4 - - - +
127B PHE* 1.3 68.1 + - - +
129B TYR* 3.0 21.4 + - - +
130B THR* 3.9 1.9 + - - +
133B ILE* 4.1 24.2 - - + +
136B MET* 4.0 18.5 - - - +
138B PHE* 3.4 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET* 2.6 45.4 + - + +
124B PHE* 3.4 19.3 - + + +
126B LEU* 1.3 72.1 - - - +
128B SER* 1.3 52.9 + - - +
130B THR* 2.8 28.4 + - - -
136B MET* 4.4 11.0 - - + -
148B LEU* 4.5 2.2 - - + -
160B LEU* 4.2 9.0 - - + -
163B MET 4.6 0.2 - - - -
164B ALA* 3.6 37.2 - - + -
167B TYR* 3.5 44.9 - + + -
168B CYS* 3.7 31.2 - - - -
194B LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE 3.1 12.4 + - - -
125B HIS* 2.6 25.4 + - - -
126B LEU 3.1 1.0 + - - -
127B PHE* 1.3 74.8 - - - +
129B TYR* 1.3 73.2 + - - +
130B THR* 3.2 8.6 + - - +
167B TYR* 4.4 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR 5.3 0.3 + - - -
95B PHE 4.3 0.2 - - - -
96B ASN* 3.5 34.2 + - - +
97B PHE* 3.8 24.9 - + + -
98B GLY* 3.4 17.9 - - - +
125B HIS* 3.2 61.4 - + - -
126B LEU* 3.0 12.9 + - - +
128B SER* 1.3 84.1 + - - +
130B THR* 1.3 74.8 + - - +
131B ASP* 3.0 2.3 + - - +
132B ALA* 3.0 27.5 + - + +
133B ILE* 4.4 7.0 - - + -
----------------------------------------------------------
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