Contacts of the strand formed by residues 118 - 131 (chain A) in PDB entry 1QZG
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 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.9 10.5 - - - +
114A SER* 3.6 0.7 - - - -
115A TYR* 2.9 33.5 + - - +
116A ARG* 3.8 9.4 + - - +
117A ASP* 1.3 89.5 + - + +
119A THR* 1.3 66.3 + - - +
120A GLN* 3.6 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER 3.1 25.4 - - - +
34A GLN* 3.4 16.3 + - - +
35A GLU 3.0 24.0 + - - +
36A LEU* 3.7 10.1 - - - +
37A GLN* 4.5 2.4 + - + +
83A LEU* 3.5 17.0 - - + +
84A GLN* 4.6 5.0 + - - +
112A LEU* 3.9 23.6 - - + -
113A ARG 3.4 12.5 + - - +
114A SER* 4.5 2.0 + - - +
118A ARG* 1.3 78.3 - - - +
120A GLN* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.4 2.0 - - - -
84A GLN* 3.0 40.8 - - - +
86A HIS* 3.4 15.2 + - + -
111A THR 3.6 0.3 - - - +
112A LEU* 3.5 2.6 - - - -
113A ARG* 2.7 72.9 + - - +
115A TYR* 3.9 15.3 - - + -
118A ARG 4.5 4.0 - - - +
119A THR* 1.3 78.1 - - - +
121A GLY* 1.3 69.9 + - - +
122A LEU* 3.3 7.2 - - - +
280A TMP 3.3 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.5 2.0 - - - +
84A GLN 2.8 14.1 + - - +
85A ILE* 3.3 12.2 - - - +
86A HIS 2.8 29.1 + - - -
110A ILE* 3.9 11.2 - - - -
111A THR 3.2 7.6 - - - -
112A LEU* 4.4 6.3 - - - -
120A GLN* 1.3 75.1 - - - +
122A LEU* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 3.6 17.9 - - + -
88A PHE* 4.6 5.6 - - + -
110A ILE* 3.8 2.8 - - - +
111A THR* 2.7 41.5 + - + +
113A ARG* 3.4 35.0 - - + +
120A GLN* 3.3 24.0 - - + +
121A GLY* 1.3 85.7 - - - +
123A SER* 1.3 63.8 + - - +
2C G 3.5 54.5 - - + +
4C T 4.8 3.8 - - + -
5C A 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS 3.0 8.1 + - - -
87A LEU* 3.7 20.4 - - - +
88A PHE* 2.9 35.0 + - - +
110A ILE* 3.8 12.2 - - - +
121A GLY 4.2 0.2 - - - -
122A LEU* 1.3 72.0 - - - +
124A LYS* 1.3 59.9 + - - +
125A ASP* 3.9 0.3 + - - +
127A PHE* 3.6 24.7 - - - -
2C G 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.1 31.8 - - + +
88A PHE 5.0 0.5 - - - +
109A GLN* 3.1 41.3 + - + +
111A THR* 3.4 13.9 - - - +
122A LEU 3.6 0.2 + - - -
123A SER* 1.3 76.8 + - - +
125A ASP* 1.3 66.3 + - - +
126A GLN* 3.2 20.9 - - - +
127A PHE* 3.1 19.8 + - - +
1C G 3.0 33.3 + - - +
2C G 3.3 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE 5.1 2.2 - - - +
90A LYS* 3.5 29.7 - - - +
91A GLN* 4.7 4.2 - - - +
124A LYS* 1.3 71.1 - - - +
126A GLN* 1.3 70.7 + - + +
127A PHE* 4.7 0.2 - - - -
150A ARG* 3.0 28.1 + - - -
1C G 2.8 40.7 + - - +
2C G 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 5.9 0.7 - - - -
108A HIS* 5.5 0.3 + - - -
109A GLN* 3.6 28.2 + - + +
124A LYS* 3.6 14.0 - - - +
125A ASP* 1.3 97.4 + - + +
127A PHE* 1.3 67.5 + - - +
128A ARG* 3.2 29.3 + - - +
150A ARG* 4.0 2.0 - - - +
1C G 3.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.0 13.2 - - + -
88A PHE 3.4 22.0 - - - -
95A LEU* 3.8 16.2 - - + -
96A PRO* 4.1 7.9 - - + -
107A LEU* 4.1 23.8 - - + -
108A HIS 3.2 16.2 - - - +
109A GLN* 3.5 17.2 - - - +
110A ILE* 4.5 1.8 - - + -
123A SER* 3.6 16.2 - - - -
124A LYS 3.1 21.8 + - - +
125A ASP 3.4 1.2 - - - -
126A GLN* 1.3 79.9 - - - +
128A ARG* 1.3 76.3 + - - +
129A TYR* 4.2 17.3 - + - -
150A ARG* 3.0 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 4.8 6.0 + - - +
107A LEU* 3.7 0.5 - - - -
108A HIS* 2.9 41.3 + - + +
126A GLN* 3.2 27.9 + - - +
127A PHE* 1.3 98.6 + - - +
129A TYR* 1.3 65.4 + - - +
149A PRO 3.9 12.6 + - - -
150A ARG* 3.2 37.9 - - - +
151A LEU 4.7 4.0 - - - -
152A MET* 3.3 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP 4.0 5.6 - - - -
96A PRO* 3.4 44.8 - - + +
105A LEU* 3.9 5.6 - - + -
106A LEU 3.1 13.9 - - - +
107A LEU* 3.9 14.8 - - + -
127A PHE* 4.2 3.8 - + + -
128A ARG* 1.3 78.1 - - - +
130A ALA* 1.3 69.6 + - - +
131A LEU* 4.0 10.3 - - + -
146A GLN* 2.8 32.5 + - - +
147A PRO* 3.6 11.3 + - - +
150A ARG* 2.9 32.9 + - + -
151A LEU* 3.4 34.9 - - + +
152A MET* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.4 4.9 - - - +
106A LEU* 2.9 37.9 + - + -
129A TYR* 1.3 77.2 - - - +
131A LEU* 1.3 59.9 + - - +
132A TRP* 3.5 28.6 - - + -
151A LEU* 5.2 2.2 - - - -
152A MET* 4.4 7.9 - - + +
154A THR* 3.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 5.1 0.9 - - + -
96A PRO* 4.9 0.9 - - + -
97A VAL 3.6 24.2 - - - +
98A ILE* 4.5 11.9 - - + -
103A GLN* 3.0 39.3 - - + +
104A PRO 3.1 19.1 - - - +
105A LEU* 3.9 21.3 - - + -
129A TYR* 4.0 19.3 - - + -
130A ALA* 1.3 74.3 - - - +
132A TRP* 1.3 67.2 + - - +
143A LEU* 3.5 32.5 - - + +
146A GLN* 3.8 8.0 - - + +
151A LEU* 5.5 1.6 - - - +
----------------------------------------------------------
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