Contacts of the strand formed by residues 86 - 97 (chain T) in PDB entry 4C4K
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 GLY 86 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4T PRO* 4.5 2.7 - - - -
5T PRO* 3.2 12.2 - - - +
82T GLY* 3.5 1.2 - - - -
83T ASN* 3.1 32.1 + - - +
84T GLU 3.6 1.0 + - - -
85T PHE* 1.3 79.9 - - - +
87T SER* 1.3 59.8 + - - -
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Residues in contact with SER 87 (chain T).
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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4T PRO* 5.4 0.9 - - - +
5T PRO* 3.9 8.7 - - - +
81T LEU 3.1 15.3 - - - -
82T GLY* 4.3 3.4 - - - -
86T GLY* 1.3 75.2 - - - -
88T ASP* 1.3 65.2 + - - +
89T SER* 6.1 0.2 - - - -
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Residues in contact with ASP 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T PRO 3.5 19.7 + - - +
6T LYS* 3.4 9.3 - - - +
7T ILE* 2.7 44.6 + - + +
79T LEU 4.1 0.2 - - - +
80T SER* 3.4 1.2 - - - -
81T LEU* 2.8 35.6 + - + +
87T SER* 1.3 75.8 - - - +
89T SER* 1.3 73.8 + - - +
1103T EDO 5.0 3.8 - - - -
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Residues in contact with SER 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T ILE* 3.6 3.8 - - - -
78T THR* 3.3 13.5 - - - +
79T LEU 3.2 5.6 - - - -
80T SER* 2.8 23.5 + - - -
87T SER* 6.1 0.2 - - - -
88T ASP* 1.3 85.7 + - - +
90T ALA* 1.3 63.8 + - - +
91T THR* 5.2 0.2 + - - -
1103T EDO 5.8 0.9 - - - -
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Residues in contact with ALA 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T ILE* 3.5 15.2 - - + +
10T LEU* 3.6 20.8 - - + +
78T THR* 3.4 2.0 - - - +
79T LEU 2.8 33.1 + - - -
89T SER* 1.3 76.4 + - - +
91T THR* 1.3 63.5 + - - +
1103T EDO 3.9 26.9 - - - -
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Residues in contact with THR 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T LEU* 3.9 4.8 - - - +
11T PRO 3.8 7.6 - - - +
12T SER* 4.1 9.5 - - - +
76T LEU* 3.6 38.1 - - + -
77T TYR 3.4 6.5 - - - +
78T THR* 2.7 30.3 + - - +
90T ALA* 1.3 77.5 - - - +
92T VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T LEU* 3.9 18.3 - - + +
11T PRO* 3.3 27.8 - - + +
12T SER 3.8 3.1 - - - -
13T ASP 4.2 1.1 - - - +
14T ILE* 3.8 35.4 - - + -
24T VAL* 5.0 4.0 - - + -
38T TRP* 4.5 8.3 - - + -
64T LEU* 5.6 0.2 - - + -
75T GLY 3.7 0.2 - - - +
76T LEU* 3.5 1.2 - - - -
77T TYR* 2.9 53.4 + - + +
91T THR* 1.3 74.8 - - - +
93T ASN* 1.3 65.3 + - - +
94T ILE* 3.7 12.0 + - + -
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Residues in contact with ASN 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T SER 2.9 10.7 + - - +
13T ASP* 3.3 16.4 - - - +
14T ILE 3.0 23.7 + - - -
75T GLY* 3.6 16.3 - - - +
76T LEU* 3.7 23.3 - - + +
91T THR 4.3 0.2 - - - -
92T VAL* 1.3 70.4 - - - +
94T ILE* 1.3 65.9 + - - +
95T HIS* 3.4 25.9 + - - -
1100T EDO 3.3 29.4 + - - -
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Residues in contact with ILE 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ILE* 3.4 29.6 - - + +
16T ILE* 4.2 13.5 - - + -
22T LEU* 4.1 24.2 - - + -
24T VAL* 4.6 1.3 - - + -
64T LEU* 4.3 7.2 - - + -
66T ILE* 4.2 10.5 - - + -
73T ASP 4.9 2.7 - - - +
74T GLY* 3.3 5.5 - - - -
75T GLY* 2.9 36.4 + - - +
77T TYR* 3.5 34.3 - - + -
92T VAL* 4.2 13.7 - - + -
93T ASN* 1.3 75.3 + - - +
95T HIS* 1.3 62.4 + - - +
96T ILE* 4.0 19.7 - - + -
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Residues in contact with HIS 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T ASP* 2.8 30.0 + - + -
14T ILE 2.9 15.8 + - - -
15T SER* 3.2 20.1 - - - +
16T ILE* 2.9 28.4 + - - +
74T GLY* 5.0 0.2 - - - -
93T ASN* 3.4 41.2 + - - -
94T ILE* 1.3 72.5 + - - +
96T ILE* 1.3 64.4 + - - +
97T ARG* 5.6 0.4 - - + -
1100T EDO 4.4 7.4 - - - -
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Residues in contact with ILE 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T ILE* 3.2 15.9 - - + +
18T GLU* 3.8 22.7 - - + +
66T ILE* 6.4 0.2 - - + -
69T VAL* 3.5 35.2 - - + -
70T GLN 3.6 11.2 - - - +
71T LYS* 3.3 42.1 + - + +
73T ASP* 4.1 4.9 - - + -
74T GLY* 3.5 36.5 - - - +
94T ILE* 4.0 9.6 - - + -
95T HIS* 1.3 78.3 - - - +
97T ARG* 1.3 62.1 + - - +
98T SER 3.9 0.2 + - - -
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Residues in contact with ARG 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O ARG* 4.7 14.1 - - - +
90O GLU* 4.7 8.9 + - - -
92O PHE* 6.2 0.2 - - - -
15T SER* 3.5 37.2 + - - +
16T ILE* 2.8 15.2 + - - +
17T ASP* 2.7 57.0 + - - +
18T GLU* 3.0 27.7 + - - +
95T HIS* 6.2 0.4 - - + -
96T ILE* 1.3 73.0 - - - +
98T SER* 1.3 60.8 + - - +
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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