Contacts of the strand formed by residues 13 - 19 (chain A) in PDB entry 1X1R
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 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU 3.9 2.0 + - - -
12A PRO* 1.3 75.0 - - - +
14A TYR* 1.3 71.0 + - - +
15A LYS* 4.4 6.1 - - + +
51A LEU* 5.0 0.9 - - + -
62A ILE* 3.2 34.3 - - + +
64A ASP* 4.0 26.9 - - + +
86A ASP* 3.4 11.3 - - - +
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Residues in contact with TYR 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 PRO* 3.7 26.3 - - + +
13A THR* 1.3 76.8 - - - +
15A LYS* 1.3 62.5 - - - +
16A LEU* 3.6 21.2 + - + +
61A ALA* 3.3 34.1 - - + -
62A ILE 2.8 8.7 + - - -
63A LEU* 3.5 15.3 - - + -
64A ASP 3.0 22.2 + - - -
86A ASP* 3.6 5.6 - - + -
172A VAL* 3.6 26.2 - - + -
175A ILE* 3.9 33.0 - - + -
176A ARG* 3.0 33.4 + - + +
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Residues in contact with LYS 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 THR* 3.9 6.4 - - + +
14A TYR* 1.3 70.5 - - - +
16A LEU* 1.3 59.4 + - - +
17A VAL* 5.0 0.2 - - + -
64A ASP* 3.2 26.5 - - + +
80A GLN* 2.9 20.1 + - - +
81A TYR* 3.5 35.2 - - + -
84A THR* 2.8 39.1 + - - +
85A GLY* 3.7 9.3 - - - +
86A ASP* 2.7 48.3 + - - +
87A GLY 3.3 6.8 + - - +
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Residues in contact with LEU 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 TYR* 3.8 16.2 - - + +
15A LYS* 1.3 78.4 - - - +
17A VAL* 1.3 64.9 + - - +
18A VAL* 5.8 0.7 - - + -
63A LEU* 4.4 11.2 - - + -
64A ASP 2.8 7.8 + - - +
65A VAL* 3.2 23.6 - - + +
66A LEU* 2.9 24.9 + - - +
81A TYR* 4.7 0.7 - - - -
87A GLY 3.3 4.5 - - - +
89A LEU* 6.0 0.9 - - + -
168A PHE* 4.2 27.8 - - + +
171A LEU* 3.8 23.6 - - + -
172A VAL* 4.3 18.8 - - + -
175A ILE* 3.6 32.1 - - + -
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Residues in contact with VAL 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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16A LEU* 1.3 79.8 - - - +
18A VAL* 1.3 64.7 + - - +
19A VAL* 3.7 11.7 + - + -
66A LEU* 3.8 11.9 - - + +
68A THR* 3.8 24.5 - - + -
81A TYR* 3.5 37.9 - - + +
82A MET* 4.1 12.1 - - - -
85A GLY* 4.4 7.2 - - - -
87A GLY 3.0 9.1 + - - +
88A PHE* 3.3 24.2 - - + +
89A LEU* 3.0 24.0 + - - +
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Residues in contact with VAL 18 (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 LEU* 5.3 1.1 - - + -
17A VAL* 1.3 74.0 - - - +
19A VAL* 1.3 54.5 + - - +
26A LYS* 3.7 29.7 - - + +
29A LEU* 5.8 2.7 - - + -
30A THR* 3.8 20.0 - - - +
65A VAL* 4.0 16.4 - - + -
66A LEU 2.9 17.7 + - - +
67A ASP* 4.4 3.8 - - - -
68A THR* 2.7 35.2 + - - +
89A LEU* 3.7 14.4 - - + -
91A VAL* 3.8 21.1 - - + -
168A PHE* 4.1 15.9 - - + -
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Residues in contact with VAL 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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17A VAL* 3.8 24.2 - - + +
18A VAL* 1.3 77.5 - - - +
20A GLY* 1.3 59.8 + - - +
26A LYS* 3.5 6.4 - - - +
68A THR* 3.7 12.8 - - + +
82A MET* 4.3 16.2 - - + -
88A PHE* 4.3 5.4 - - + -
89A LEU 2.9 17.7 + - - +
90A ILE* 4.0 20.2 - - + -
91A VAL* 2.8 29.8 + - - +
106A PHE* 3.9 25.8 - - + -
109A LEU* 6.3 0.2 - - + -
110A ILE* 4.3 9.2 - - + -
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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