Contacts of the strand formed by residues 10 - 18 (chain C) in PDB entry 5JTP
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 THR 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C MET* 1.3 69.2 + - - +
11C PHE* 1.3 60.8 + - - +
12C GLN* 5.6 3.6 - - + +
85C SER* 3.4 5.1 - - - +
86C ILE* 3.1 9.1 - - - +
87C ALA* 3.0 47.3 + - + +
88C GLY* 4.9 0.5 - - - -
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Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PRO* 3.7 29.1 - - + +
9C MET* 3.3 31.2 + - + +
10C THR* 1.3 74.3 - - - +
12C GLN* 1.3 64.1 + - - +
13C ILE* 4.1 22.0 - - + -
84C PHE* 3.5 37.7 - + + -
85C SER 3.6 0.9 - - - -
86C ILE* 4.4 12.1 - - + -
97C CYS* 4.6 2.2 - - - -
101C TYR* 3.7 32.8 - + + +
102C CYS* 3.6 27.1 - - - -
105C ILE* 4.9 9.4 - - + -
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PRO* 5.5 1.6 - - - -
10C THR* 5.7 3.8 - - + -
11C PHE* 1.3 80.0 - - - +
13C ILE* 1.3 72.3 + - - +
14C GLN* 3.4 20.3 + - - +
84C PHE* 3.5 3.1 - - - -
85C SER* 3.0 43.8 + - - +
468E LEU* 6.4 0.2 - - - +
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Residues in contact with ILE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.9 11.2 - - - +
127A ASN* 3.5 38.1 - - + +
128A LEU 3.8 22.7 - - - +
129A ALA* 6.1 0.4 - - - -
130A PRO* 4.6 9.4 - - + +
11C PHE* 4.1 12.0 - - + -
12C GLN* 1.3 82.8 + - - +
14C GLN* 1.3 63.8 + - - +
15C ARG 3.9 4.0 - - - +
16C ILE* 3.7 18.4 - - + -
84C PHE* 3.8 21.1 - - + -
105C ILE* 3.9 26.0 - - + -
468E LEU* 5.6 6.2 - - - +
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Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASN* 5.1 0.9 + - - -
12C GLN* 3.4 31.9 + - - +
13C ILE* 1.3 75.7 - - - +
15C ARG* 1.4 66.1 + - + +
55C VAL* 5.6 2.3 - - + +
83C ILE* 3.0 33.6 + - + +
85C SER* 2.9 49.3 + - - +
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Residues in contact with ARG 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN* 4.0 8.7 - - - +
127A ASN* 4.0 6.7 - - - +
13C ILE* 3.7 1.8 - - - +
14C GLN* 1.4 85.9 - - + +
16C ILE* 1.3 63.0 + - - +
17C TYR* 3.6 16.2 - - + -
82C GLY* 3.5 1.0 - - - -
83C ILE* 2.8 36.2 + - + -
32D PHE* 3.5 56.5 + - - +
35D ASP* 4.6 15.2 + - - +
122D THR* 2.7 49.0 + - - +
123D PHE* 4.7 0.8 - - - +
124D PRO* 5.7 1.4 - - - +
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN* 2.7 35.1 + - - +
127A ASN* 3.2 21.9 - - - +
13C ILE* 3.7 18.4 - - + -
15C ARG* 1.3 72.5 - - - +
17C TYR* 1.3 69.5 + - - +
80C GLN* 3.4 17.0 - - - +
81C GLY 3.8 3.6 - - - -
84C PHE* 4.2 5.4 - - + -
105C ILE* 3.5 30.3 - - + -
106C LEU* 3.7 22.0 - - + -
109C TYR* 3.4 42.4 - - + +
122D THR* 3.3 1.7 - - - +
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Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN* 4.9 0.7 - - - +
15C ARG* 3.6 22.7 - - + -
16C ILE* 1.3 82.5 - - - +
18C THR* 1.3 65.4 + - - +
19C LYS* 3.2 29.2 - - + -
80C GLN* 3.2 11.6 - - - +
81C GLY* 2.8 38.0 + - - +
82C GLY 4.6 3.1 - - - -
83C ILE* 3.3 33.9 - - + +
25D ALA* 5.4 0.2 - - + -
28D ALA* 3.4 17.7 - - + -
29D PRO* 3.3 19.6 - - - +
32D PHE* 3.5 30.5 - + - -
120D ARG 3.3 14.6 - - - +
121D GLY 3.9 3.6 - - - +
122D THR* 3.6 14.4 - - + +
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 1.3 77.2 - - - +
19C LYS* 1.4 62.2 + - - +
20C ASP 3.6 4.0 + - - -
21C ILE* 3.5 24.6 - - - +
78C VAL* 4.1 3.1 - - + -
79C GLN 3.7 5.4 - - - -
80C GLN* 3.3 25.1 - - - +
113C CYS* 3.6 25.4 - - - -
23D PHE* 3.7 14.9 - - - -
25D ALA* 4.1 2.8 - - - +
120D ARG* 3.0 16.4 + - + +
121D GLY* 3.3 22.7 + - - -
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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