Contacts of the strand formed by residues 111 - 119 (chain A) in PDB entry 1QX3
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 ARG 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 4.0 2.8 - - - -
43A GLU* 2.8 42.3 + - - +
45A GLY* 3.9 18.3 - - - -
46A LEU* 3.2 32.5 - - - +
84A GLU* 3.8 6.5 + - - -
86A ARG* 4.7 2.6 - - - +
106A GLU* 3.0 26.5 + - - +
107A ASP 3.7 14.7 + - - +
108A HIS* 2.9 49.5 + - + +
109A SER 3.2 0.2 - - - -
110A LYS* 1.3 81.7 - - + +
112A SER* 1.3 62.9 + - - +
113A SER 4.0 5.6 - - - +
151A LEU* 5.0 0.4 - - + +
154A LYS* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS 3.9 4.4 - - - +
39A MET* 3.5 36.4 + - - +
41A TYR* 3.0 39.9 + - - +
43A GLU 2.8 14.1 + - - -
44A MET* 3.3 12.6 + - - -
111A ARG* 1.3 72.6 - - - +
113A SER* 1.3 63.0 + - - +
154A LYS* 3.6 9.6 - - - +
155A PRO* 3.6 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 4.3 6.6 - - - +
44A MET 2.9 9.1 + - - -
45A GLY* 3.4 20.7 - - - -
46A LEU 3.9 1.0 + - - -
83A TYR* 2.8 29.9 + - - -
111A ARG* 3.3 8.8 - - - +
112A SER* 1.3 81.3 - - - +
114A PHE* 1.3 65.2 + - - +
115A VAL* 4.7 0.2 - - - +
151A LEU* 4.3 7.0 - - - +
154A LYS* 4.6 4.7 - - - -
155A PRO* 3.3 28.7 - - - -
157A LEU* 5.4 2.9 - - - -
273A LEU* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.9 18.6 - - + -
48A ILE* 3.8 20.4 - - + -
100A MET* 5.1 2.5 - - - -
103A VAL* 3.5 23.3 - - + -
108A HIS* 4.4 11.4 - + - -
113A SER* 1.3 79.5 - - - +
115A VAL* 1.3 79.0 + - - +
116A CYS* 3.9 20.9 - - + -
143A PHE* 3.5 39.5 - + - -
151A LEU* 3.9 22.0 - - + -
155A PRO 3.1 7.7 + - - +
156A LYS* 4.7 6.3 - - + -
157A LEU* 2.9 27.7 + - - +
158A PHE* 4.0 17.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU 2.9 13.9 + - - +
47A CYS* 3.2 18.6 - - + -
48A ILE 2.8 23.3 + - - -
78A PHE* 3.9 23.8 - - + -
83A TYR* 3.7 32.8 - - + +
113A SER* 4.7 0.9 - - - +
114A PHE* 1.3 87.1 - - - +
116A CYS* 1.3 65.6 + - - +
117A VAL* 4.2 2.0 - - + -
157A LEU* 3.4 25.1 - - + +
159A ILE* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.1 10.5 - - + +
50A ILE* 3.9 9.4 - - - -
100A MET* 4.1 17.9 - - - -
114A PHE* 3.9 20.6 - - + -
115A VAL* 1.3 77.0 - - - +
117A VAL* 1.3 64.8 + - - +
118A LEU* 3.6 29.6 + - - +
139A ILE* 5.4 0.2 - - - -
157A LEU 2.9 6.5 + - - -
158A PHE* 3.4 21.7 - - + +
159A ILE* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A CYS* 4.3 4.7 - - - -
48A ILE 2.7 13.7 + - - +
49A ILE* 3.5 17.5 - - + +
50A ILE* 2.9 28.2 + - - +
74A LEU* 3.4 37.5 - - + -
78A PHE* 4.8 1.1 - - + -
115A VAL* 4.2 9.9 - - + -
116A CYS* 1.3 77.4 - - - +
118A LEU* 1.3 66.6 + - - +
119A LEU* 3.9 13.9 - - + -
159A ILE* 3.3 38.6 - - + +
216A ILE* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.8 24.2 - - + -
96A ILE* 5.5 5.8 - - + -
100A MET* 5.6 0.9 - - - -
116A CYS* 3.6 28.7 - - - +
117A VAL* 1.3 72.7 - - - +
119A LEU* 1.3 62.4 + - - +
120A SER* 4.1 1.1 - - - +
127A ILE* 4.0 24.2 - - + -
136A LEU* 3.6 30.1 - - + -
139A ILE* 5.0 13.7 - - + -
158A PHE* 5.2 5.6 - - + -
159A ILE 2.9 11.1 + - - +
160A ILE* 4.0 17.2 - - + +
161A GLN* 2.9 31.8 + - - +
162A ALA* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.1 11.4 - - + -
50A ILE* 3.0 13.0 + - - +
51A ASN* 3.7 22.9 - - + +
52A ASN* 3.0 20.3 + - - +
64A ARG* 3.4 11.5 + - - +
67A THR* 4.1 1.1 - - - +
70A ASP* 4.1 8.3 - - + +
71A ALA* 3.9 26.2 - - + +
74A LEU* 4.0 10.8 - - + -
117A VAL* 3.9 17.7 - - + -
118A LEU* 1.3 78.0 - - - +
120A SER* 1.3 65.5 + - - +
161A GLN* 3.5 30.7 - - + -
216A ILE* 4.0 13.7 - - + -
----------------------------------------------------------
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