Contacts of the strand formed by residues 134 - 140 (chain A) in PDB entry 1RI5
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 PHE 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A SER* 3.0 21.8 - - - +
68A VAL 3.5 21.8 - - - -
69A LEU* 3.6 20.0 - - + -
89A GLU* 5.7 3.6 - - + -
90A TYR 5.5 0.4 - - - -
91A TYR* 3.4 46.9 - + + -
130A LEU* 4.0 19.5 - - + -
132A LYS* 3.5 34.1 - - + -
133A GLU* 1.3 78.4 - - - +
135A ASP* 1.3 64.2 + - - +
136A VAL 3.9 11.0 - - - +
137A ILE* 4.5 2.5 - - + -
163A HIS* 2.8 19.1 + + + +
164A LEU* 3.6 5.9 - - - +
165A ARG* 3.0 25.3 + - - -
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Residues in contact with ASP 135 (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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63A LYS* 4.4 8.3 + - - +
65A GLY 4.5 2.3 - - - +
66A ASP* 3.5 33.1 - - - +
67A SER* 2.9 38.8 + - - +
134A PHE* 1.3 73.7 - - - +
136A VAL* 1.3 63.7 + - + +
164A LEU* 4.3 0.7 - - - -
165A ARG* 3.3 36.9 + - - +
168A GLY* 3.2 8.9 - - - -
169A TYR* 3.1 22.5 + - - -
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Residues in contact with VAL 136 (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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61A TYR* 3.3 26.9 - - + +
62A THR* 4.3 12.6 - - + -
66A ASP* 4.1 14.4 - - - +
67A SER 3.2 4.3 + - - +
68A VAL* 3.2 21.7 - - + +
69A LEU 3.0 23.2 + - - -
82A TYR* 5.6 0.4 - - - +
134A PHE* 3.3 1.3 - - - +
135A ASP* 1.3 86.9 - - + +
137A ILE* 1.3 72.8 + - - +
138A SER 4.7 0.4 - - - +
169A TYR* 3.4 18.6 - - + +
171A ILE* 4.2 25.4 - - + -
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Residues in contact with ILE 137 (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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69A LEU* 3.4 29.4 - - + +
71A LEU* 3.9 24.0 - - + -
134A PHE* 4.5 1.8 - - + -
136A VAL* 1.3 77.0 - - - +
138A SER* 1.3 60.6 + - - +
160A ILE* 3.4 34.8 - - + +
163A HIS* 3.8 21.8 - - + +
164A LEU* 3.8 15.3 - - + -
169A TYR 2.9 10.4 + - - +
170A PHE* 3.3 29.5 - - + -
171A ILE* 2.9 25.8 + - - +
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Residues in contact with SER 138 (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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58A ILE* 5.3 0.5 - - - +
68A VAL* 4.7 2.2 - - - -
69A LEU 2.8 11.5 + - - +
70A ASP* 3.4 11.1 + - - +
71A LEU* 2.8 33.4 + - - +
82A TYR* 3.0 27.8 + - - -
136A VAL* 4.1 0.8 - - - -
137A ILE* 1.3 75.6 - - - +
139A SER* 1.3 58.3 + - - +
140A GLN* 2.8 33.1 + - - +
171A ILE* 3.4 14.1 - - - +
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Residues in contact with SER 139 (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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71A LEU* 3.6 10.8 - - - -
124A TYR* 2.7 27.0 + - - -
138A SER* 1.3 77.3 + - - +
140A GLN* 1.3 60.2 + - - +
141A PHE 3.8 0.9 + - - -
142A SER* 3.4 3.3 + - - -
143A PHE* 3.3 23.8 + - - +
170A PHE* 3.9 22.0 - - - -
171A ILE 3.0 8.4 + - - -
172A MET* 3.1 22.6 - - - +
173A THR 3.2 4.2 + - - +
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Residues in contact with GLN 140 (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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54A LYS* 3.5 26.6 - - - +
57A LEU* 4.2 6.7 - - - +
58A ILE* 6.0 3.4 - - + -
70A ASP* 5.1 5.0 + - - +
71A LEU 4.3 3.8 + - - -
72A GLY 4.5 7.9 + - - +
78A ASP* 3.7 20.2 - - - +
138A SER* 2.8 26.8 + - - +
139A SER* 1.3 72.7 + - - +
141A PHE* 1.3 83.4 + - + +
142A SER* 3.3 5.8 + - - -
171A ILE* 3.6 25.5 - - - +
173A THR* 2.7 41.5 + - - +
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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