Contacts of the strand formed by residues 87 - 93 (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 GLY 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS 3.3 4.9 + - - +
16A LEU* 3.3 5.0 - - - -
17A VAL* 3.0 24.9 + - - +
85A GLY 3.5 1.6 - - - -
86A ASP* 1.3 80.5 - - - +
88A PHE* 1.3 68.7 + - - -
119A PHE* 3.9 0.6 - - - -
120A PRO* 3.3 12.6 - - - -
171A LEU* 3.7 17.7 - - - -
175A ILE* 4.0 5.7 - - - +
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Residues in contact with PHE 88 (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* 3.3 38.6 - - + +
19A VAL* 4.3 6.3 - - + -
81A TYR 4.5 1.3 - - - -
82A MET* 3.6 47.1 - - + -
85A GLY* 4.5 4.5 - - - -
87A GLY* 1.3 76.7 - - - -
89A LEU* 1.3 62.5 + - - +
90A ILE* 4.7 0.2 - - + -
110A ILE* 3.6 50.0 - - + -
113A VAL* 6.5 0.2 - - + -
114A LYS* 4.3 6.3 - - + -
119A PHE* 3.6 28.5 - + - -
120A PRO 3.0 9.7 + - - +
121A MET* 3.0 10.4 - - + +
122A ILE 3.0 23.4 + - - -
171A LEU* 3.7 9.7 - - - +
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Residues in contact with LEU 89 (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* 6.0 0.9 - - + -
17A VAL 3.0 9.4 + - - +
18A VAL* 3.7 13.9 - - + -
19A VAL* 2.9 31.1 + - - +
29A LEU* 6.2 2.9 - - + -
88A PHE* 1.3 70.8 - - - +
90A ILE* 1.3 61.1 + - - +
91A VAL* 3.7 8.9 + - + +
122A ILE* 3.7 20.9 - - + -
124A VAL* 4.1 10.3 - - + -
167A THR* 3.6 33.7 - - + +
168A PHE* 3.8 37.7 - - + -
171A LEU* 3.8 29.3 - - + +
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Residues in contact with ILE 90 (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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19A VAL* 3.6 7.6 - - + +
88A PHE* 3.9 3.1 - - + -
89A LEU* 1.3 73.5 - - - +
91A VAL* 1.3 62.9 + - - +
103A VAL* 3.9 30.7 - - + +
106A PHE* 3.9 23.3 - - + -
107A HIS* 4.1 21.1 - - + +
110A ILE* 3.8 31.4 - - + -
121A MET* 3.9 24.7 - - + -
122A ILE 3.0 11.9 + - - +
123A LEU* 3.6 8.8 - - + +
124A VAL 2.9 25.1 + - - -
150A ILE* 5.1 5.8 - - + -
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Residues in contact with VAL 91 (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 VAL* 3.8 24.9 - - + -
19A VAL 2.8 17.0 + - - +
20A GLY* 3.5 19.6 - - - -
21A ASP 4.2 0.5 + - - -
24A VAL* 3.6 28.3 - - + +
26A LYS* 4.3 3.1 - - + -
29A LEU* 4.0 26.5 - - + -
89A LEU* 4.2 9.4 - - + +
90A ILE* 1.3 80.7 - - - +
92A TYR* 1.3 73.0 + - - +
99A SER 4.9 1.4 - - - +
103A VAL* 5.1 0.5 - - - +
106A PHE* 5.8 0.2 - - - -
124A VAL* 3.4 18.8 - - + +
126A ASN* 4.0 7.4 - - + -
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Residues in contact with TYR 92 (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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24A VAL* 3.8 8.7 - - - -
91A VAL* 1.3 74.1 - - - +
93A SER* 1.3 69.4 + - - +
94A VAL* 4.0 9.4 - - + +
99A SER* 3.5 28.9 - - - +
100A PHE* 3.6 31.4 - + + -
103A VAL* 3.8 8.1 - - + -
123A LEU* 3.8 35.0 - - + -
124A VAL 2.9 13.0 + - - +
125A ALA* 3.4 31.9 - - + +
126A ASN* 2.8 29.5 + - - +
134A ARG* 5.7 0.2 + - - -
136A VAL* 3.8 17.0 - - + +
137A THR 4.8 0.5 + - - -
141A GLY* 3.3 25.5 - - - -
152A TYR* 3.5 2.4 + - - -
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Residues in contact with SER 93 (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 GLY 4.7 0.9 - - - -
24A VAL* 3.6 22.2 - - - +
92A TYR* 1.3 80.0 - - - +
94A VAL* 1.3 58.9 + - - +
95A THR* 2.8 27.8 + - - -
96A ASP* 3.0 37.1 + - - +
99A SER* 3.0 11.6 + - - -
126A ASN 3.6 5.2 - - - -
127A LYS* 3.4 19.8 + - - +
136A VAL* 4.4 0.7 - - - +
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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