Contacts of the strand formed by residues 105 - 115 (chain A) in PDB entry 1QXT
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 ASN 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 4.6 8.1 - - + +
98A ILE 3.3 11.7 - - - +
99A SER* 4.0 16.4 - - - +
104A GLY* 1.3 77.9 - - - +
106A TYR* 1.3 58.8 + - - +
107A LYS* 3.8 23.7 - - - +
126A LYS 3.6 1.4 - - - +
127A GLY* 3.4 1.9 - - - -
128A ILE* 2.9 58.4 + - - +
129A ASP* 4.9 4.4 + - - +
130A PHE* 3.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.9 19.3 - - + -
55A VAL* 3.4 20.0 - - + +
59A THR* 2.9 46.5 + - - -
60A LEU* 3.9 13.9 - - + -
63A THR* 4.4 4.0 - - - -
96A ALA 3.6 1.6 - - - +
97A THR* 3.3 7.4 - - - +
98A ILE* 2.8 49.9 + - + +
100A PHE* 3.7 21.3 - + - -
105A ASN* 1.3 72.4 - - - +
107A LYS* 1.3 61.4 + - - +
108A THR* 3.9 0.7 - - + -
125A LEU* 3.9 24.5 - - + -
126A LYS 3.5 2.5 - - - -
127A GLY* 3.8 8.5 - - - -
130A PHE* 3.5 28.9 - + - -
136A ILE* 3.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 3.7 3.4 - - - -
97A THR* 4.8 12.6 - - + +
105A ASN* 3.8 21.3 - - - +
106A TYR* 1.3 72.0 - - - +
108A THR* 1.3 58.7 - - - +
124A GLU 4.0 0.7 - - - +
125A LEU* 3.5 1.4 - - - -
126A LYS* 2.8 67.1 + - + +
128A ILE* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.6 30.5 - - + +
66A TYR* 2.8 25.1 + - - -
95A GLU* 3.3 6.9 - - - +
96A ALA* 2.8 47.8 + - - +
98A ILE* 3.9 10.7 - - + +
106A TYR* 4.3 1.8 - - + -
107A LYS* 1.3 78.8 - - - +
109A ARG* 1.3 61.5 + - - +
123A ILE* 4.6 1.3 - - - -
124A GLU 3.3 7.2 - - - -
125A LEU* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 4.0 0.9 - - - -
93A VAL* 3.6 35.6 - - + +
94A GLN 3.3 10.5 - - - +
95A GLU* 4.0 19.9 + - + -
108A THR* 1.3 76.4 - - - +
110A ALA* 1.3 70.6 + - - +
111A GLU* 5.0 12.1 + - - +
122A ARG 4.1 0.3 - - - +
123A ILE* 3.5 2.0 - - - +
124A GLU* 2.9 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.9 6.3 + - + +
93A VAL* 3.4 7.1 - - - +
94A GLN* 2.8 67.3 + - + +
109A ARG* 1.3 80.0 - - - +
111A GLU* 1.3 61.0 + - - +
112A VAL* 4.0 4.0 - - + -
121A ASN* 5.7 0.4 - - + -
122A ARG 3.2 11.2 - - - +
123A ILE* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR 3.8 2.2 - - - -
93A VAL* 4.7 7.3 - - + +
109A ARG* 5.0 13.7 + - - +
110A ALA* 1.3 72.1 - - - +
112A VAL* 1.3 60.9 + - - +
113A LYS* 3.4 32.7 + - + +
120A VAL 3.6 2.4 - - - +
121A ASN* 3.6 2.8 - - - -
122A ARG* 2.9 74.9 + - + +
188A ILE* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY* 3.2 22.4 - - - +
88A MET* 3.8 20.9 - - + -
90A GLU 4.2 0.3 - - - +
91A GLY* 3.1 3.5 - - - -
92A TYR* 2.9 49.9 + - + +
94A GLN* 3.6 37.2 - - + +
110A ALA* 4.6 2.7 - - + -
111A GLU* 1.3 74.3 - - - +
113A LYS* 1.3 65.0 + - - +
119A LEU* 4.1 6.1 - - + -
120A VAL 3.4 3.1 - - - +
121A ASN* 3.3 22.9 - - - +
188A ILE* 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.3 3.6 - - - -
89A PRO 3.6 6.1 - - - +
90A GLU* 3.4 20.6 - - - +
91A GLY* 4.2 3.1 - - - -
111A GLU* 3.4 31.0 + - + +
112A VAL* 1.3 77.3 - - - +
114A PHE* 1.3 69.7 + - - +
115A GLU* 3.6 34.3 + - + -
119A LEU* 3.6 8.0 - - - +
120A VAL* 2.9 35.6 + - + +
122A ARG* 5.5 3.1 - - - +
188A ILE* 4.8 4.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
7A LEU* 4.1 31.0 - - + -
8A PHE* 3.5 36.8 - + - -
12A VAL* 3.9 30.3 - - + -
88A MET* 3.9 23.6 - - + -
89A PRO* 3.0 30.9 + - + +
113A LYS* 1.3 79.4 - - - +
115A GLU* 1.3 66.7 + - - +
116A GLY 3.6 20.8 + - - +
117A ASP* 4.0 9.9 - - - -
118A THR 3.3 15.9 - - - -
119A LEU* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 3.6 34.5 + - + -
114A PHE* 1.3 76.5 - - - +
116A GLY* 1.3 60.8 + - - +
117A ASP 3.6 0.3 + - - -
118A THR* 2.8 26.1 + - - -
120A VAL* 3.8 31.2 - - + -
122A ARG* 6.1 0.7 - - - -
----------------------------------------------------------
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