Contacts of the strand formed by residues 94 - 102 (chain A) in PDB entry 3UP1
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LYS* 3.4 4.1 - - - -
91A VAL* 2.9 37.8 + - + +
92A GLY 3.5 0.2 - - - -
93A GLU* 1.3 85.7 - - + +
95A SER* 1.3 66.0 + - - +
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Residues in contact with SER 95 (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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88A CYS* 3.6 14.5 - - - -
89A VAL 3.6 5.2 - - - -
90A LYS* 3.1 27.4 + - - +
94A LYS* 1.3 73.6 - - - +
96A LEU* 1.3 62.7 + - - +
98A CYS* 3.9 18.4 - - - -
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Residues in contact with LEU 96 (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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15A LEU* 4.9 20.1 - - + +
18A TYR* 4.0 38.4 - - + -
49A LEU* 5.0 2.0 - - + -
89A VAL* 2.8 32.6 + - + +
91A VAL* 4.0 24.9 - - + -
94A LYS 3.5 2.0 + - - -
95A SER* 1.3 75.8 - - - +
97A THR* 1.3 65.3 + - + +
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Residues in contact with THR 97 (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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15A LEU* 5.2 16.8 - - + +
18A TYR* 4.0 17.0 - - + +
19A SER* 5.9 0.2 - - - -
20A PHE* 4.3 6.8 - - + -
87A ILE 4.2 0.2 - - - +
88A CYS* 3.4 1.0 - - - -
89A VAL* 2.9 46.7 + - + +
96A LEU* 1.3 92.7 - - + +
98A CYS* 1.3 69.8 + - - +
99A LYS* 6.0 0.2 - - - +
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Residues in contact with CYS 98 (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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20A PHE* 4.7 0.9 - - - -
86A ASN* 3.6 17.7 - - - +
87A ILE 3.2 5.6 - - - +
88A CYS* 2.1 47.8 - - - -
95A SER* 3.9 14.8 - - - -
97A THR* 1.3 83.8 + - - +
99A LYS* 1.3 69.2 + - - +
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Residues in contact with LYS 99 (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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20A PHE* 3.6 51.2 + - + +
21A SER* 4.7 6.7 - - - +
22A CYS 5.6 0.2 - - - +
85A SER 3.6 0.9 - - - +
86A ASN* 3.3 5.1 - - - +
87A ILE* 2.9 29.9 + - - -
98A CYS* 1.3 79.2 - - - +
100A LYS* 1.3 64.7 + - - +
101A ILE* 3.6 28.7 + - + +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 4.3 28.6 + - + +
85A SER 3.2 9.4 - - - +
86A ASN* 3.5 18.6 + - + +
99A LYS* 1.3 73.6 - - - +
101A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 101 (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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20A PHE* 4.8 0.4 - - + -
22A CYS* 4.3 18.8 - - + +
84A LYS* 3.8 3.5 - - - +
85A SER* 2.7 42.6 + - - +
87A ILE* 3.6 30.3 - - + -
99A LYS* 3.9 38.4 - - + +
100A LYS* 1.3 80.2 - - - +
102A ASP* 1.3 72.4 + - - +
103A LEU* 3.5 6.3 + - + +
105A THR* 4.9 1.1 - - - +
106A ILE* 3.8 31.6 - - + -
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Residues in contact with ASP 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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81A LEU 5.1 1.2 - - - +
83A GLY* 3.7 29.3 + - - +
84A LYS* 3.9 21.4 - - + +
101A ILE* 1.3 75.1 - - - +
103A LEU* 1.3 59.4 + - - +
104A THR* 2.7 35.0 + - - +
105A THR* 2.8 48.8 + - + +
106A ILE* 4.0 1.0 - - - +
192A TYR* 5.4 3.1 + - - -
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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