Contacts of the strand formed by residues 118 - 128 (chain A) in PDB entry 1QYO
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 THR 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.4 33.2 - - + +
15A LEU* 3.8 34.5 - - + -
114A PHE* 3.4 4.5 - - - -
115A GLU* 2.8 41.6 + - - +
116A GLY 3.3 1.0 - - - -
117A ASP* 1.3 79.8 + - - +
119A LEU* 1.3 68.0 + - - +
120A VAL* 3.6 3.0 + - + -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.7 0.9 - - + -
12A VAL* 4.1 6.5 - - + +
13A PRO 2.9 10.3 + - - +
14A ILE* 3.3 9.2 - - + +
15A LEU 3.0 23.6 + - - -
68A VAL* 3.6 30.7 - - + -
70A CYS* 3.8 7.0 - - - -
71A PHE* 3.7 34.3 - - + -
88A MET* 3.8 31.2 - - + -
112A VAL* 3.7 13.7 - - + -
113A LYS 3.7 17.9 - - - +
114A PHE* 4.0 14.5 - - + -
118A THR* 1.3 70.9 - - - +
120A VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.4 32.1 - - + +
17A GLU* 6.0 3.6 - - + +
111A GLU 3.6 1.5 - - - +
112A VAL* 3.2 8.5 - - - +
113A LYS* 2.8 41.6 + - + +
115A GLU* 3.8 33.0 - - + -
118A THR* 4.1 4.9 - - + +
119A LEU* 1.3 80.6 - - - +
121A ASN* 1.3 63.8 + - - +
122A ARG* 3.7 28.7 - - + -
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Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU 3.0 11.4 + - - +
16A VAL* 3.5 8.7 - - + +
17A GLU 2.9 27.4 + - - +
63A THR 3.5 20.3 - - - +
64A LEU 3.9 8.0 - - - +
67A GLY* 3.6 12.4 + - - -
68A VAL* 3.8 20.3 - - + +
110A ALA* 3.4 30.1 - - - +
111A GLU 3.7 1.3 - - - -
112A VAL* 3.4 16.9 - - + +
120A VAL* 1.3 74.4 - - - +
122A ARG* 1.3 59.6 + - - +
123A ILE* 3.5 10.5 + - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.5 14.8 - - + +
109A ARG 3.9 1.0 - - - +
110A ALA* 3.2 3.3 - - - -
111A GLU* 3.0 53.4 + - + +
115A GLU* 6.1 0.9 - - - -
120A VAL* 3.7 22.0 - - + -
121A ASN* 1.3 69.7 - - - +
123A ILE* 1.3 60.9 + - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.8 20.9 - - + -
17A GLU 2.7 12.0 + - - +
18A LEU* 3.4 21.4 - - + -
19A ASP* 2.9 28.9 + - - +
63A THR* 3.5 49.6 - - + +
64A LEU* 4.1 2.0 - - + -
108A THR* 4.3 5.2 - - + -
109A ARG 3.5 10.8 - - - +
110A ALA* 3.9 9.0 - - + -
121A ASN* 3.5 28.5 - - - +
122A ARG* 1.3 73.0 - - - +
124A GLU* 1.3 76.7 - - - +
125A LEU 4.6 0.2 - - - +
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP* 3.4 14.4 - - + +
107A LYS 3.9 1.2 - - - +
108A THR* 3.4 4.0 - - - -
109A ARG* 2.9 57.1 + - + +
123A ILE* 1.3 78.3 - - - +
125A LEU* 1.3 60.0 - - - +
126A LYS 4.3 0.2 - - - -
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.3 13.5 - - + -
19A ASP 2.8 13.1 + - - +
20A GLY* 3.3 5.6 - - - -
21A ASP* 3.0 25.5 + - - +
22A VAL* 3.7 31.0 - - + -
27A PHE* 4.1 11.2 - - + -
60A LEU* 3.7 26.2 - - + -
63A THR* 4.3 11.7 - - + +
106A TYR* 4.0 26.5 - - + -
107A LYS 3.6 2.5 - - - -
108A THR* 3.8 24.2 - - + -
123A ILE* 4.1 0.8 - - + -
124A GLU* 1.3 74.8 - - - +
126A LYS* 1.3 62.7 + - - +
127A GLY 4.2 0.9 - - - +
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASP* 3.5 31.7 + - + +
105A ASN* 3.7 1.7 - - - +
106A TYR* 3.4 1.2 - - - -
107A LYS* 2.8 50.0 + - + +
125A LEU* 1.3 77.8 - - - +
127A GLY* 1.3 60.8 + - - +
128A ILE* 4.0 26.0 + - + +
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 2.7 18.1 + - - +
22A VAL* 3.4 7.2 - - - +
23A ASN* 3.0 23.9 + - - -
105A ASN 3.2 9.4 - - - -
106A TYR* 4.0 8.5 - - - -
125A LEU 4.2 0.2 - - - -
126A LYS* 1.3 74.8 + - - +
128A ILE* 1.3 65.9 + - - +
130A PHE* 3.9 15.7 - - - -
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.8 3.1 - - - -
104A GLY* 3.2 1.7 - - - -
105A ASN* 3.0 59.9 + - - +
107A LYS* 6.1 4.3 - - + -
126A LYS* 4.0 30.5 - - + +
127A GLY* 1.3 79.7 - - - +
129A ASP* 1.3 80.3 + - - +
130A PHE* 3.3 4.7 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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