Contacts of the strand formed by residues 146 - 153 (chain B) in PDB entry 1QXR
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 PHE 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR 3.7 1.2 - - - +
72B VAL 3.7 0.2 - - - -
73B LEU* 2.7 54.9 + - + +
101B ALA* 4.5 11.4 - - + -
103B LYS 3.4 15.5 - - - -
104B GLY* 4.4 3.4 - - - -
105B LYS 3.8 6.5 - - - +
106B GLY* 3.6 23.6 - - - -
107B GLY 3.8 3.8 - - - -
122B MET* 3.6 44.2 - - + -
138B THR* 4.3 9.4 - - - -
139B VAL 3.8 22.0 - - - -
140B ASN* 3.3 22.8 - - + +
145B PRO* 1.3 71.2 - - - +
147B ILE* 1.3 60.8 + - - +
148B PHE* 3.7 21.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE 4.8 1.6 - - - +
13B GLU 3.5 27.1 - - - +
14B THR* 3.7 15.5 - - - +
15B GLY* 3.6 24.0 - - - +
70B THR* 5.2 0.7 - - - -
71B THR 3.3 9.0 - - - +
72B VAL* 4.3 17.0 - - + -
101B ALA* 4.1 1.4 - - - +
102B LEU* 2.9 37.7 + - + +
103B LYS* 2.8 33.1 + - + +
145B PRO* 4.3 14.8 - - + +
146B PHE* 1.3 80.7 - - - +
148B PHE* 1.3 70.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.2 5.4 - - - -
71B THR* 3.0 64.8 + - + -
73B LEU* 4.7 4.5 - - + -
99B TYR* 3.2 32.3 - + + -
100B VAL 3.3 15.0 - - - +
101B ALA* 4.0 8.1 - - + -
102B LEU* 4.1 7.2 - - - +
122B MET* 4.6 6.5 - - + -
138B THR* 3.2 37.9 - - + -
146B PHE* 3.7 26.2 - + + -
147B ILE* 1.3 80.0 - - - +
149B LEU* 1.3 64.1 + - - +
150B ALA* 4.6 4.3 - - + -
301B PA5 3.6 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 5.9 0.4 - - + -
100A VAL* 3.7 36.6 - - + -
127A VAL* 4.5 8.1 - - + -
10B VAL* 5.2 6.3 - - + -
12B PHE* 6.0 0.9 - - + -
17B ILE* 4.9 1.3 - - + -
68B PHE* 4.3 16.6 - - + -
69B ALA 3.5 23.6 - - - +
70B THR* 3.7 20.0 - - + -
98B VAL 4.0 0.7 - - - +
99B TYR* 3.4 2.4 - - - +
100B VAL* 2.7 50.5 + - + +
102B LEU* 4.2 13.9 - - + +
148B PHE* 1.3 76.0 - - - +
150B ALA* 1.3 65.2 + - - +
151B ILE* 4.3 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.1 7.3 - - - +
69B ALA 2.7 43.6 + - - +
97B GLU* 3.6 20.6 - - - +
98B VAL 3.5 3.6 - - - -
99B TYR* 3.9 26.5 - - + -
148B PHE* 4.2 2.2 - - + -
149B LEU* 1.3 75.3 - - - +
151B ILE* 1.3 60.3 + - - +
152B TYR* 3.9 2.8 - - + -
301B PA5 4.1 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.6 3.9 - - - +
98A VAL* 4.1 26.9 - - + -
151A ILE* 3.3 54.3 - - + -
66B LEU* 4.2 13.9 - - + -
67B ASN 3.5 12.6 - - - +
68B PHE* 4.0 11.7 - - + -
97B GLU* 3.4 3.6 - - - +
98B VAL* 2.9 40.9 + - + +
100B VAL* 4.5 9.6 - - + -
149B LEU* 4.3 19.7 - - + -
150B ALA* 1.3 78.8 - - - +
152B TYR* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.4 1.3 - - - -
56B ALA* 4.5 0.9 - - - +
58B GLU* 2.5 32.2 + - - +
66B LEU* 3.6 6.7 - - - +
67B ASN* 2.9 59.2 + - + +
68B PHE* 4.1 3.3 + - - -
69B ALA* 4.1 18.6 - - + +
90B HIS* 4.8 4.5 - + - +
97B GLU* 3.3 26.5 - - + +
150B ALA 3.9 14.4 - - - -
151B ILE* 1.3 76.5 - - - +
153B PRO* 1.3 87.9 - - + +
156B ALA* 5.1 4.3 - - + -
157B GLY 6.2 0.4 - - - -
158B HIS* 5.0 14.3 - + - -
301B PA5 3.2 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY* 3.5 28.3 - - - +
66A LEU* 4.1 13.7 - - + -
64B GLY* 6.1 2.2 - - - +
65B ASP 3.7 8.1 - - - +
66B LEU* 4.0 4.2 - - + -
67B ASN* 4.5 0.2 + - - -
95B ARG* 3.6 21.5 - - + +
96B ALA 2.9 21.1 - - - +
152B TYR* 1.3 95.8 - - + +
154B ALA* 1.3 60.0 + - - +
155B ASP* 3.6 8.5 - - - +
156B ALA* 3.0 28.7 + - + +
157B GLY 4.8 0.3 + - - -
----------------------------------------------------------
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