Contacts of the strand formed by residues 10 - 16 (chain C) in PDB entry 1JT7
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 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ASN 4.2 6.4 - - - +
8C TYR 4.2 2.3 - - - +
9C LYS* 1.3 89.0 - - + +
11C PRO* 1.3 77.8 - - + +
12C LYS* 3.6 35.5 - - - +
44C PHE 4.7 0.3 - - - +
45C GLN* 3.9 7.0 + - - -
46C LEU 5.4 0.9 + - - -
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Residues in contact with PRO 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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9C LYS 4.6 0.7 - - - +
10C LYS* 1.3 96.0 - - + +
12C LYS* 1.3 69.6 + - - +
43C GLN* 5.0 2.5 - - + -
44C PHE 3.0 20.4 - - - +
45C GLN* 3.7 15.2 - - - +
59C THR* 4.3 12.8 - - + -
137C VAL* 3.6 29.8 + - + +
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Residues in contact with LYS 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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7C ASN* 3.9 30.3 - - + +
10C LYS* 3.6 35.4 - - - +
11C PRO* 1.3 83.8 + - - +
13C LEU* 1.3 66.9 + - - +
14C LEU* 5.1 1.7 - - + +
42C ILE 3.8 0.5 - - - +
43C GLN* 3.8 2.3 - - - -
44C PHE* 2.7 38.4 + - - +
46C LEU* 4.9 13.0 - - + -
134C PRO* 4.1 24.0 - - + +
135C LEU 3.3 16.2 - - - +
136C PRO* 4.4 13.9 - - + +
137C VAL* 3.6 8.1 - - - -
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Residues in contact with LEU 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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12C LYS* 1.3 75.5 - - - +
14C LEU* 1.3 62.6 + - - +
15C TYR 3.7 0.4 - - - -
22C PHE* 3.9 25.6 - - + -
37C ARG* 3.7 35.0 - - + +
42C ILE* 3.4 37.2 - - + +
43C GLN* 4.2 5.4 - - + +
133C LEU 3.5 0.3 - - - +
134C PRO* 3.1 6.8 - - - +
135C LEU* 2.7 38.6 + - + +
136C PRO 3.8 20.9 - - - +
137C VAL* 3.6 21.5 - - + -
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Residues in contact with LEU 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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12C LYS* 4.2 2.4 + - + +
13C LEU* 1.3 77.2 - - - +
15C TYR* 1.3 61.2 - - - +
16C CYS 3.7 1.0 + - - -
22C PHE* 3.6 3.0 - - - +
23C LEU* 2.9 57.2 + - + +
42C ILE 4.5 4.0 + - - -
44C PHE* 4.4 11.6 - - + -
46C LEU* 4.4 16.4 - - + -
56C ILE* 4.0 35.7 - - + -
97C TYR* 3.9 31.0 - - + +
109C LEU* 5.3 0.9 - - + -
132C PHE* 4.0 15.4 - - + -
133C LEU 4.0 0.4 - - - -
134C PRO* 4.1 20.2 - - + -
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Residues in contact with TYR 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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13C LEU 3.7 0.4 - - - -
14C LEU* 1.3 71.7 - - - +
16C CYS* 1.3 71.7 + - - +
17C SER* 3.5 11.4 + - - -
20C GLY* 3.2 36.8 - - - -
21C HIS 3.6 6.7 - - - -
22C PHE* 3.5 32.5 - + + -
94C TYR* 6.4 0.4 - + - -
132C PHE* 3.3 5.1 - - - -
133C LEU* 2.9 59.7 + - + +
135C LEU* 3.6 22.2 - - + -
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Residues in contact with CYS 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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14C LEU 3.7 1.2 + - - -
15C TYR* 1.3 73.2 - - - +
17C SER* 1.3 62.6 + - - +
18C ASN* 3.3 24.0 + - - -
19C GLY 4.8 1.3 - - - +
20C GLY* 3.0 31.9 + - - -
21C HIS* 2.8 19.7 + - + +
111C LEU* 3.8 22.9 - - + -
129C ALA 3.3 26.9 - - - -
131C LEU 3.6 10.3 - - - -
132C PHE* 3.5 17.5 - - + -
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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