Contacts of the strand formed by residues 12 - 22 (chain A) in PDB entry 1QYF
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 VAL 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU 3.6 23.3 - - - +
8A PHE* 4.5 6.1 - - + -
10A GLY 3.7 12.3 - - - +
11A VAL* 1.3 78.6 - - - +
13A PRO* 1.3 81.5 - - + +
14A ILE* 3.8 0.9 - - - +
34A GLU* 3.2 4.6 - - - -
35A GLY 2.9 31.0 + - - -
71A PHE* 3.7 29.2 - - + -
114A PHE* 3.8 25.6 - - + -
117A ASP 3.9 3.6 - - - +
119A LEU* 4.1 2.7 - - + -
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Residues in contact with PRO 13 (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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11A VAL* 4.2 5.1 - - + +
12A VAL* 1.3 87.4 - - - +
14A ILE* 1.3 60.7 + - - +
15A LEU* 6.2 0.4 - - + -
33A GLY 3.6 8.5 - - - +
34A GLU* 4.3 3.8 - - + -
117A ASP* 3.6 17.9 - - + +
118A THR* 3.5 23.2 - - + +
119A LEU 2.9 24.8 + - - -
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Residues in contact with ILE 14 (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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12A VAL 3.8 2.9 - - - +
13A PRO* 1.3 79.9 - - - +
15A LEU* 1.3 70.8 + - - +
16A VAL* 4.0 15.3 - - + -
32A GLU* 3.5 5.1 - - - -
33A GLY 2.9 32.8 + - - +
34A GLU 3.5 7.6 - - - +
35A GLY 3.4 19.3 - - - +
42A LEU* 3.6 18.6 - - + -
44A LEU* 3.8 21.8 - - + -
68A VAL* 4.6 15.0 - - + -
71A PHE* 3.4 35.0 - - + -
119A LEU* 3.3 10.5 - - + +
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Residues in contact with LEU 15 (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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13A PRO* 6.4 0.4 - - + -
14A ILE* 1.3 81.1 - - - +
16A VAL* 1.3 64.5 + - - +
17A GLU* 4.3 7.9 - - + +
31A GLY 3.5 3.4 - - - +
32A GLU* 4.0 24.2 - - + -
118A THR* 3.6 23.8 - - + -
119A LEU 3.0 6.3 + - - +
120A VAL* 3.2 23.6 - - + +
121A ASN* 2.8 25.5 + - - +
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Residues in contact with VAL 16 (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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14A ILE* 4.0 17.9 - - + -
15A LEU* 1.3 79.2 - - - +
17A GLU* 1.3 71.7 + - - +
18A LEU 5.0 0.2 - - - +
29A VAL 4.5 0.4 - - - +
30A SER* 3.4 1.9 - - - -
31A GLY 2.8 35.0 + - - +
44A LEU* 4.4 7.4 - - + -
46A PHE* 3.9 22.0 - - + -
64A LEU* 3.8 35.7 - - + +
68A VAL* 5.1 1.6 - - + -
121A ASN* 3.2 11.9 - - + +
123A ILE* 3.7 26.7 - - + -
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Residues in contact with GLU 17 (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* 4.3 7.8 - - + +
16A VAL* 1.3 79.4 - - - +
18A LEU* 1.3 56.0 + - - +
28A SER* 6.1 0.7 - - - -
29A VAL 3.5 2.9 - - - +
30A SER* 2.6 35.7 + - - -
31A GLY 4.6 2.6 + - - +
120A VAL* 5.9 3.1 - - + -
121A ASN 2.9 11.6 + - - +
122A ARG* 3.4 15.8 - - + +
123A ILE* 2.8 33.7 + - - +
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Residues in contact with LEU 18 (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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16A VAL 4.3 0.2 - - - -
17A GLU* 1.3 75.6 + - - +
19A ASP* 1.3 82.5 + - - +
20A GLY* 3.6 2.5 - - - +
27A PHE* 3.5 33.7 - - + -
28A SER* 3.1 7.1 - - - -
29A VAL* 2.8 43.3 + - + +
60A LEU* 4.9 6.5 - - + -
63A THR* 3.7 30.3 - - + -
64A LEU* 4.0 22.4 - - + -
123A ILE* 3.4 20.6 - - + +
125A LEU* 4.4 12.8 - - + -
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Residues in contact with ASP 19 (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* 1.3 79.7 - - - +
20A GLY* 1.3 58.8 - - - +
27A PHE 3.6 2.9 - - - +
28A SER* 2.7 27.5 + - - -
122A ARG* 5.9 0.9 + - - -
123A ILE 3.0 9.3 + - - +
124A GLU* 3.4 13.8 - - + +
125A LEU 2.9 24.3 + - - +
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Residues in contact with GLY 20 (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* 3.6 4.6 - - - +
19A ASP* 1.3 75.1 - - - +
21A ASP* 1.3 61.3 + - - +
26A LYS* 3.3 6.4 - - - +
27A PHE* 2.7 59.3 + - - +
125A LEU* 3.4 9.6 - - - -
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Residues in contact with ASP 21 (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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20A GLY* 1.3 75.2 - - - +
22A VAL* 1.3 56.3 + - - +
23A ASN 3.9 0.5 + - - -
24A GLY* 2.9 33.0 + - - -
25A HIS 3.4 4.7 - - - -
26A LYS* 4.1 25.3 - - + +
27A PHE* 4.0 0.6 - - - -
125A LEU* 3.1 9.5 + - - +
126A LYS* 3.4 30.0 + - + +
127A GLY 2.7 31.2 + - - +
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Residues in contact with VAL 22 (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* 1.3 77.4 + - - +
23A ASN* 1.3 67.0 + - - +
25A HIS* 2.8 39.8 + - + +
27A PHE* 3.9 14.8 - - + -
54A PRO* 5.5 0.4 - - + -
55A VAL* 3.9 25.8 - - + -
106A TYR* 3.8 12.8 - - + -
125A LEU* 3.5 26.0 - - + -
127A GLY* 3.4 4.5 - - - -
130A PHE* 3.7 29.6 - - + -
137A LEU* 4.3 11.9 - - + -
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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