Contacts of the strand formed by residues 101 - 108 (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 ARG 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLY 3.1 26.3 + - - -
100A SER* 1.3 72.4 - - - +
102A VAL* 1.3 66.2 + - - +
158A LEU 5.6 0.4 + - - -
193A GLU* 4.0 40.1 + - + +
194A ALA* 2.6 22.0 - - - +
195A VAL* 3.2 25.4 - - - +
225A LEU* 4.4 1.0 - - - +
226A ILE* 3.6 40.7 + - + +
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Residues in contact with VAL 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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100A SER* 4.2 14.4 - - - +
101A ARG* 1.3 82.4 - - - +
103A ARG* 1.3 56.6 + - - +
104A TYR* 5.4 1.3 - - + -
192A GLY 2.9 1.0 - - - +
193A GLU* 2.5 37.0 - - - -
194A ALA* 2.9 36.6 + - + +
196A ILE* 4.7 15.0 - - + -
223A LEU* 3.6 21.5 - - + -
224A ALA 2.8 27.1 - - - +
225A LEU* 4.5 3.4 - - - -
226A ILE* 4.7 2.2 - - - +
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Residues in contact with ARG 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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102A VAL* 1.3 69.8 - - - +
104A TYR* 1.3 65.1 + - - +
191A ASP* 5.0 2.2 - - - +
192A GLY 3.1 5.6 - - - +
222A SER* 3.7 3.3 + - - +
223A LEU* 2.5 39.2 - - - -
224A ALA* 2.8 33.2 + - + +
225A LEU 5.8 0.7 - - - +
226A ILE* 5.3 1.4 - - - +
198I THR* 3.8 33.7 + - - +
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Residues in contact with TYR 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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102A VAL* 4.4 4.0 - - + +
103A ARG* 1.3 80.7 - - - +
105A ARG* 1.3 56.2 + - - +
160A LEU 4.5 4.7 - - - +
190A PHE 3.7 0.9 - - - +
191A ASP* 2.6 41.8 - - - +
192A GLY 2.8 26.6 + - - +
193A GLU* 5.0 2.5 - - - -
194A ALA* 5.3 4.0 - - + +
221A LEU* 6.2 4.0 - - + -
222A SER 2.8 10.5 - - - +
223A LEU* 5.0 1.3 - - + -
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Residues in contact with ARG 105 (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 ARG* 3.4 42.2 + - - +
55A ILE* 3.9 20.9 + - - +
104A TYR* 1.3 75.7 - - - +
106A ILE* 1.3 61.5 + - - +
107A VAL* 3.3 41.7 - - - +
189A ARG* 3.7 41.6 - - + +
190A PHE 2.5 16.4 - - - +
191A ASP* 4.7 3.6 - - + -
220A LEU 3.6 3.6 - - - +
221A LEU* 3.9 1.7 - - - -
222A SER* 3.0 29.3 + - - -
26B ALA* 5.0 8.9 - - - +
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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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105A ARG* 1.3 78.1 - - - +
107A VAL* 1.3 57.7 + - - +
108A ALA* 3.9 4.7 - - + +
188A VAL 2.7 16.8 - - - +
189A ARG* 3.2 2.2 - - - -
190A PHE* 2.8 40.9 + - + +
210A ILE* 6.5 1.3 - - + -
219A GLY 5.0 3.1 - - - +
220A LEU 3.7 14.6 - - - +
221A LEU* 4.3 19.1 - - + -
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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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54A ARG* 4.2 6.7 - - + -
55A ILE* 4.7 12.3 - - + +
105A ARG* 3.3 35.8 - - - +
106A ILE* 1.3 64.3 - - - +
108A ALA* 1.3 51.8 + - - +
164A TYR* 5.4 0.9 - - - +
187A ALA* 3.3 30.1 - - + -
188A VAL 2.4 30.7 - - - +
189A ARG* 5.2 0.4 - - + -
217A GLY 3.1 28.0 - - - +
218A CYS* 2.9 8.9 - - - -
219A GLY* 2.7 32.7 + - - -
220A LEU 4.3 1.8 + - - -
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Residues in contact with ALA 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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106A ILE* 3.9 5.3 - - + -
107A VAL* 1.3 74.6 - - - +
109A SER* 1.3 60.6 + - - +
148A TRP* 3.4 28.7 - - + -
187A ALA* 3.1 7.8 - - - -
188A VAL* 2.8 36.7 + - + +
190A PHE* 4.3 4.5 - - + -
210A ILE 3.7 18.4 - - - +
211A GLY* 5.0 1.1 - - - -
212A ARG 5.1 0.4 - - - -
218A CYS* 3.8 11.7 - - - -
219A GLY* 5.5 0.2 - - - -
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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