Contacts of the strand formed by residues 110 - 117 (chain A) in PDB entry 5E0T
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 LYS 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASP* 5.7 4.3 - - - +
103A PHE 4.1 0.4 - - - +
105A ALA* 3.3 43.9 + - + +
107A ASN* 3.6 7.4 + - - +
108A GLN 3.5 2.2 - - - +
109A GLU* 1.3 78.7 - - - +
111A VAL* 1.3 70.6 + - - +
112A SER* 4.5 8.7 - - - +
143B GLU* 3.6 32.5 - - - +
146B ARG* 4.4 20.6 - - - +
147B ILE* 4.5 9.3 - - - +
150B ASP* 5.3 6.0 + - - -
180B ILE* 4.0 22.9 - - + -
181B LYS 3.5 3.1 - - - -
182B LEU* 3.7 19.7 - - + -
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Residues in contact with VAL 111 (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* 4.0 16.8 - - + -
103A PHE 3.4 8.7 - - - +
104A GLU* 4.5 18.8 - - + +
108A GLN 4.8 10.1 - - - +
109A GLU 5.4 0.7 - - - -
110A LYS* 1.3 80.2 - - - +
112A SER* 1.3 72.3 + - - +
113A ASP* 5.5 2.4 - - + +
179B ASN* 4.0 0.9 - - - +
180B ILE* 3.5 0.8 - - - -
181B LYS* 2.9 46.2 + - + +
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Residues in contact with SER 112 (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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81A CYS 4.9 4.4 + - - -
86A ASP* 5.7 0.2 + - - -
101A LEU 4.4 0.9 - - - -
102A VAL* 3.4 9.2 - - - +
103A PHE* 2.8 47.4 + - - +
110A LYS* 4.5 10.4 - - - +
111A VAL* 1.3 74.3 - - - +
113A ASP* 1.3 62.9 + - - +
114A TYR* 3.6 22.6 + - - -
150B ASP* 5.8 0.2 + - - -
179B ASN 3.3 8.1 - - - -
180B ILE* 3.6 22.4 - - - +
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Residues in contact with ASP 113 (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 ALA* 5.5 1.7 - - - +
101A LEU 3.6 3.6 - - - -
102A VAL* 3.8 18.9 - - + +
111A VAL* 5.5 3.1 - - + +
112A SER* 1.3 77.9 - - - +
114A TYR* 1.3 63.2 + - - +
115A GLU* 2.7 31.9 - - - +
178B GLY* 3.1 4.0 - - - -
179B ASN* 2.8 58.5 + - - +
181B LYS* 6.1 1.3 - - - -
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Residues in contact with TYR 114 (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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78A ILE* 3.7 27.8 - - + -
81A CYS* 3.4 24.6 - - + +
99A LEU 3.6 1.4 - - - +
100A ALA* 3.2 5.7 - - - +
101A LEU* 2.8 44.6 + - + +
103A PHE* 3.6 28.7 - + - -
112A SER* 3.6 23.2 - - - -
113A ASP* 1.3 79.4 + - - +
115A GLU* 1.3 65.2 + - - +
150B ASP* 4.1 1.6 + - - +
151B LEU* 3.9 8.9 - - + +
154B ILE* 3.8 31.9 - - + -
177B ASN 3.4 4.3 - - - +
178B GLY* 3.4 25.4 - - - -
179B ASN 4.9 0.2 - - - -
180B ILE* 3.7 24.5 - - + +
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Residues in contact with GLU 115 (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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78A ILE* 4.8 4.1 - - - +
98A THR* 4.7 18.6 - - + +
99A LEU 3.5 4.5 - - - +
100A ALA* 3.5 19.9 - - + +
113A ASP* 2.7 28.3 - - - +
114A TYR* 1.3 77.2 - - - +
116A MET* 1.3 59.4 + - - +
176B GLY* 3.1 7.6 - - - -
177B ASN* 2.8 49.6 + - - +
179B ASN* 5.6 0.2 + - - -
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Residues in contact with MET 116 (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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70A VAL* 4.4 12.8 - - + -
71A ASN 4.5 4.9 - - - +
74A SER* 4.2 9.2 - - - -
75A MET* 3.6 50.0 - - + -
78A ILE* 3.8 17.3 - - + -
98A THR* 3.1 7.5 - - - -
99A LEU* 2.8 68.9 + - + +
101A LEU* 4.1 8.1 - - + -
114A TYR 4.1 0.6 - - - -
115A GLU* 1.3 73.3 - - - +
117A LYS* 1.3 77.9 + - - +
118A LEU* 4.3 2.4 - - + +
119A MET* 6.1 0.4 - - + -
175B LEU 3.7 11.2 - - - +
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Residues in contact with LYS 117 (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 GLY 4.9 0.3 - - - +
70A VAL* 5.7 0.3 - - - -
71A ASN 5.5 1.9 + - - -
97A ASP 3.9 5.4 - - - +
98A THR* 4.4 7.6 - - + -
116A MET* 1.3 89.1 - - - +
118A LEU* 1.3 64.0 + - - +
119A MET* 3.9 19.6 - - + +
173B GLY 4.4 7.9 + - - -
174B GLU* 3.7 23.2 + - - +
175B LEU 3.6 12.5 + - - +
176B GLY* 4.1 14.8 - - - +
177B ASN* 5.7 3.6 - - - +
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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