Contacts of the strand formed by residues 101 - 111 (chain A) in PDB entry 1Q9S
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 ILE 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.8 32.1 - - + -
17A GLY 3.5 3.6 - - - +
18A GLN* 3.7 35.2 - - + +
19A VAL* 4.9 0.2 - - - -
60A VAL* 3.9 0.8 - - - -
61A GLY* 2.9 33.5 + - - +
99A GLY 4.4 2.7 - - - +
100A GLU* 1.3 77.4 - - - +
102A LEU* 1.3 62.3 + - - +
103A ASN* 3.8 12.0 + - - +
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Residues in contact with LEU 102 (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 ARG* 3.2 4.7 - - - -
17A GLY 2.7 33.6 + - - +
19A VAL* 3.7 12.6 - - + -
35A ALA* 4.1 14.4 - - + +
37A PHE* 3.6 25.6 - - + -
58A ALA* 4.2 6.3 - - + -
59A SER 3.4 21.5 - - - +
60A VAL* 4.0 15.9 - - + +
87A THR* 3.7 25.6 - - + +
89A ILE* 4.1 13.7 - - + -
97A PHE* 4.6 4.0 - - + -
100A GLU 3.6 1.6 + - - -
101A ILE* 1.3 71.9 - - - +
103A ASN* 1.3 60.2 + - - +
104A VAL* 3.7 22.2 - - + -
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Residues in contact with ASN 103 (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 CYS 4.0 3.4 - - - -
16A ARG* 2.6 42.6 + - - +
58A ALA* 3.1 7.8 - - - +
59A SER* 2.8 54.6 + - - +
61A GLY* 3.0 22.6 + - - -
101A ILE* 3.8 14.3 + - - +
102A LEU* 1.3 71.1 - - - +
104A VAL* 1.3 62.6 + - - +
150A PHE* 4.0 6.3 - - + -
151A PHE* 3.6 4.8 - - + -
154A SER* 3.4 12.3 + - - +
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Residues in contact with VAL 104 (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 PHE* 3.1 4.3 - - - -
15A CYS* 2.8 44.2 + - - +
37A PHE* 4.3 7.9 - - + -
57A TRP 3.6 1.1 - - - -
58A ALA* 3.7 18.6 - - + -
68A MET* 3.7 21.1 - - + -
85A MET* 4.2 14.6 - - + -
87A THR* 4.2 6.1 - - - +
102A LEU* 3.7 23.3 - - + -
103A ASN* 1.3 80.3 - - - +
105A ALA* 1.3 70.0 + - - +
106A ILE* 4.0 13.9 - - + -
150A PHE* 3.6 8.5 - - - -
151A PHE* 4.3 0.4 - - - -
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Residues in contact with ALA 105 (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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12A PRO* 4.7 1.8 - - + -
13A TYR 3.2 5.6 - - - -
14A PHE* 3.6 30.3 - - + -
56A GLY* 3.4 1.9 - - - -
57A TRP* 3.1 31.3 + - + +
68A MET* 3.7 1.0 - - - +
104A VAL* 1.3 75.5 - - - +
106A ILE* 1.3 64.4 + - - +
107A VAL* 3.3 3.7 - - + +
145A ILE* 4.2 12.3 - - + -
151A PHE* 3.7 17.2 - - + -
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Residues in contact with ILE 106 (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 LEU* 3.5 10.2 - - + +
12A PRO* 2.9 4.7 - - - +
13A TYR* 2.8 60.7 + - + +
45A LEU* 5.2 0.9 - - + -
49A ILE* 5.1 5.2 - - + -
54A TYR* 3.3 44.6 - - + -
55A TYR 4.2 2.9 - - - -
68A MET* 4.7 1.8 - - - -
70A VAL* 4.4 10.5 - - + -
72A ILE* 4.0 18.8 - - + -
85A MET* 3.8 23.1 - - + -
104A VAL* 4.0 13.9 - - + -
105A ALA* 1.3 72.3 - - - +
107A VAL* 1.3 60.2 + - - +
108A GLY 4.5 0.9 - - - +
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Residues in contact with VAL 107 (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 LEU* 3.5 20.5 - - - +
12A PRO* 4.1 5.4 - - + -
55A TYR* 3.2 29.5 + - + -
56A GLY* 3.6 11.7 - - - -
57A TRP* 3.8 20.6 - - + -
105A ALA 3.3 17.9 - - - +
106A ILE* 1.3 74.4 - - - +
108A GLY* 1.3 61.5 + - - +
137A LEU* 4.1 4.0 - - + -
142A TYR* 3.8 33.6 + - + -
145A ILE* 3.8 19.5 - - + -
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Residues in contact with GLY 108 (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 LEU* 3.7 7.2 - - - +
54A TYR* 3.1 13.4 - - - +
55A TYR* 3.0 50.6 + - - -
106A ILE* 4.5 0.2 - - - +
107A VAL* 1.3 83.2 - - - +
109A TYR* 1.3 60.7 + - - -
142A TYR* 5.3 0.9 - - - -
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Residues in contact with TYR 109 (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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9A ARG* 4.1 20.0 - - - +
11A LEU* 4.4 4.1 - - + +
50A SER* 5.1 3.4 - - - -
51A THR 3.9 9.6 + - - -
52A GLY* 3.9 14.8 - - - -
53A ILE 3.7 9.0 - - - -
54A TYR* 3.7 25.5 - + + -
55A TYR* 3.9 0.4 - - - -
108A GLY* 1.3 72.8 - - - -
110A LEU* 1.3 64.1 + - - +
111A ARG* 3.3 28.5 - - - -
112A PRO* 3.1 32.9 - - + +
136A ARG* 3.5 18.0 + - - -
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Residues in contact with LEU 110 (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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53A ILE* 2.9 19.1 + - + +
54A TYR 4.4 7.2 - - - +
55A TYR* 3.4 35.2 - - + -
69A VAL* 4.3 11.4 - - + -
108A GLY 3.9 0.2 + - - -
109A TYR* 1.3 79.1 - - - +
111A ARG* 1.3 67.7 + - + +
129A ASP* 3.5 44.6 - - + +
132A GLU* 3.7 28.9 - - + -
133A ALA 4.6 1.6 - - - +
136A ARG* 3.9 14.6 + - - +
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Residues in contact with ARG 111 (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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53A ILE* 2.7 37.9 + - + +
109A TYR* 3.3 14.7 - - - -
110A LEU* 1.3 82.9 - - - +
112A PRO* 1.3 94.4 + - + +
114A LYS* 3.8 31.1 - - - +
116A PHE* 4.4 1.8 - - - -
125A ALA* 4.0 23.9 - - - +
126A ILE* 4.4 1.2 - - - +
129A ASP* 2.9 41.3 + - - +
401A FMN 3.0 41.2 + - - -
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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