Contacts of the strand formed by residues 188 - 196 (chain A) in PDB entry 5U07
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ILE 2.7 3.3 - - - +
107A VAL* 2.4 40.9 - - - -
108A ALA 2.8 24.7 + - - +
110A PRO* 3.6 20.4 - - + -
164A TYR* 3.1 39.7 - - + +
165A ALA* 5.0 2.9 - - - -
166A GLN 5.5 1.8 - - - +
186A PRO* 4.9 1.8 - - + +
187A ALA* 1.3 82.1 - - - +
189A ARG* 1.3 53.5 + - - +
190A PHE* 3.2 35.4 - - + -
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Residues in contact with ARG 189 (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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105A ARG* 3.7 39.1 - - - +
106A ILE 3.2 4.7 - - - -
107A VAL* 5.2 0.4 - - + -
162A SER* 3.3 19.1 + - - +
164A TYR* 3.0 39.0 - - + +
188A VAL* 1.3 70.7 - - - +
190A PHE* 1.3 60.6 + - - +
191A ASP* 3.3 40.5 + - - +
26B ALA* 5.8 7.4 - - + -
22I LEU 5.8 0.7 - - - +
24I SER* 4.5 28.3 + - - +
25I PRO* 5.0 1.6 - - - +
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Residues in contact with PHE 190 (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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104A TYR* 4.5 1.3 - - - -
105A ARG* 2.5 37.8 - - - +
106A ILE* 2.8 42.0 + - + +
108A ALA* 4.3 2.9 - - + -
110A PRO* 5.0 2.5 - - + -
145A ALA* 4.9 7.6 - - + -
148A TRP* 3.4 37.7 - + - -
161A LEU* 3.9 17.9 - - + -
162A SER 2.7 32.3 - - - +
163A THR* 3.5 27.4 - - + -
164A TYR 4.8 2.2 - - - -
188A VAL* 3.2 35.7 - - + -
189A ARG* 1.3 73.0 - - - +
191A ASP* 1.3 52.4 + - - +
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Residues in contact with ASP 191 (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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103A ARG* 5.0 2.1 - - - +
104A TYR* 2.6 27.5 + - - +
105A ARG* 4.8 3.1 - - - -
160A LEU 3.4 5.5 - - - +
162A SER* 3.0 32.0 + - - +
189A ARG* 3.3 33.2 + - - +
190A PHE* 1.3 71.1 - - - +
192A GLY* 1.3 69.6 + - - +
198I THR* 2.9 38.9 + - - +
227I SER* 3.8 13.8 + - - -
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Residues in contact with GLY 192 (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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102A VAL 2.9 9.2 - - - +
103A ARG* 3.1 5.0 - - - -
104A TYR* 2.8 34.3 + - - +
160A LEU* 3.0 24.6 + - - -
191A ASP* 1.3 86.6 + - - +
193A GLU* 1.3 53.6 + - - -
198I THR 5.0 4.0 - - - +
227I SER* 5.1 0.9 - - - -
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Residues in contact with GLU 193 (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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101A ARG* 4.0 37.3 + - + +
102A VAL 2.5 12.3 - - - +
104A TYR* 5.2 0.7 - - - -
159A GLU* 2.9 2.6 - - - +
160A LEU* 2.8 51.0 + - + +
192A GLY* 1.3 70.5 - - - +
194A ALA* 1.3 59.6 + - - +
226A ILE* 5.3 5.7 - - - +
228I ALA* 4.4 13.7 - - - +
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Residues in contact with ALA 194 (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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100A SER 2.7 5.9 - - - +
101A ARG* 2.6 37.1 - - - -
102A VAL* 2.9 29.5 + - + +
104A TYR* 5.3 4.9 - - + +
157A GLY* 5.2 3.1 - - - -
159A GLU* 2.4 27.6 - - + -
193A GLU* 1.3 71.9 - - - +
195A VAL* 1.3 57.8 + - - +
196A ILE* 5.9 1.1 - - + -
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Residues in contact with VAL 195 (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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99A GLY* 3.4 34.3 - - - +
100A SER 3.3 3.4 - - - -
101A ARG* 3.2 26.2 - - - +
157A GLY* 3.0 25.5 - - - -
158A LEU* 2.7 52.3 + - + +
194A ALA* 1.3 75.3 - - - +
196A ILE* 1.3 67.3 + - - +
197A SER* 6.3 0.4 - - - -
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Residues in contact with ILE 196 (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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97A ASP 4.0 12.6 - - - +
98A LYS* 3.0 23.2 - - + +
99A GLY 3.0 19.3 + - - +
100A SER* 3.7 24.4 + - - +
102A VAL* 4.7 16.4 - - + -
157A GLY* 4.4 3.6 - - - -
194A ALA* 5.2 1.3 - - + +
195A VAL* 1.3 81.4 - - - +
197A SER* 1.3 63.6 + - - +
198A ASP 4.0 6.3 - - - +
199A VAL* 4.3 13.9 - - + +
202A VAL* 3.7 32.1 - - + -
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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