Contacts of the strand formed by residues 93 - 100 (chain B) in PDB entry 5UH5
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B SER* 4.2 13.5 - - - +
89B GLU* 4.8 9.2 - - + +
91B GLU 3.6 13.5 - - - +
92B PRO* 1.3 75.9 - - - +
94B THR* 1.3 70.1 + - - +
95B MET* 5.2 0.7 - - + +
113B PRO* 4.2 17.0 - - + -
114B ALA 6.1 0.2 - - - +
116B VAL* 4.2 24.7 - - + -
139B VAL* 3.8 5.0 - - - +
140B VAL* 3.1 49.4 + - + +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PRO 5.1 0.5 + - - -
93B VAL* 1.3 82.8 + - - +
95B MET* 1.3 65.7 + - - +
96B TYR* 4.2 22.7 - - + +
113B PRO* 3.4 15.3 - - - +
137B GLU* 3.7 28.3 + - + +
138B LEU 3.3 14.7 + - - +
139B VAL* 4.6 8.5 - - - +
140B VAL 5.0 0.2 - - - +
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Residues in contact with MET 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 5.0 4.7 - - - -
85B VAL* 4.4 10.3 - - + -
93B VAL* 5.2 1.3 - - + +
94B THR* 1.3 74.4 - - - +
96B TYR* 1.3 65.0 + - - +
110B ILE* 3.5 28.0 - - + -
111B VAL 3.3 16.8 - - - +
112B PRO* 4.7 3.6 - - + -
113B PRO* 3.7 10.8 - - + -
116B VAL* 3.6 30.3 - - + -
118B VAL* 4.9 4.7 - - + -
137B GLU* 3.9 0.5 - - - -
138B LEU* 2.9 60.0 + - + +
140B VAL* 3.8 24.0 - - + +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 4.2 21.8 - - + +
95B MET* 1.3 80.5 - - - +
97B LEU* 1.3 60.0 + - - +
98B ARG* 3.3 46.7 - - + +
110B ILE* 5.2 0.9 - - - -
111B VAL* 3.0 40.5 + - + +
136B VAL 3.7 9.9 - - - -
137B GLU* 4.0 28.8 + - + -
138B LEU* 5.8 0.2 - - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 5.8 3.4 - - + -
96B TYR* 1.3 73.2 - - - +
98B ARG* 1.3 68.9 + - - +
105B VAL* 3.9 23.3 - - + -
106B THR 4.0 4.7 - - - +
109B ASP* 3.3 45.1 - - + +
110B ILE* 3.7 24.9 - - + -
125B ILE* 4.1 14.4 - - + -
134B LEU* 3.8 7.1 - - + +
136B VAL* 3.1 44.0 + - + +
138B LEU* 5.1 10.1 - - + +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B TYR* 3.3 52.8 + - + +
97B LEU* 1.3 87.5 - - - +
99B LYS* 1.3 67.2 + - - +
109B ASP* 5.0 4.1 + - - +
111B VAL* 5.5 10.3 - - - +
134B LEU 3.4 7.4 - - - +
135B GLU* 4.2 31.4 - - + +
136B VAL 5.0 0.7 - - - +
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 5.3 0.4 - - + -
98B ARG* 1.3 77.7 - - - +
100B GLN* 1.3 72.4 + - - +
102B PRO 4.8 10.5 + - - -
103B GLY* 5.4 1.2 - - - -
104B GLU 4.2 15.6 + - - +
105B VAL* 3.6 29.8 - - + +
109B ASP* 3.5 36.3 - - + +
128B LEU* 3.4 11.1 - - + +
134B LEU* 3.2 28.9 + - + +
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 1.3 88.3 + - - +
101B GLY* 1.3 72.4 + - - +
102B PRO 5.0 0.7 - - - +
128B LEU* 4.6 1.6 - - - -
131B LYS* 5.2 8.9 - - - +
132B GLY 3.2 20.9 - - - +
133B LYS* 3.9 34.2 + - + +
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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