Contacts of the strand formed by residues 10 - 15 (chain C) in PDB entry 1Z83
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 ILE 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LEU 4.0 18.4 - - - +
8C THR* 3.4 16.0 + - + +
9C ASN* 1.3 77.9 - - - +
11C ILE* 1.3 64.0 + - - +
12C PHE* 4.0 26.2 - - + -
80C MET* 4.0 21.5 - - + -
90C PHE* 3.7 4.9 - - + -
92C ILE* 4.0 15.3 - - + -
105C PHE* 4.0 17.5 - - + -
109C ILE* 4.3 3.6 - - + -
110C GLY* 4.2 10.5 - - - +
111C GLN 4.3 5.8 - - - +
112C PRO* 3.6 11.7 - - + +
113C THR* 2.8 35.4 + - - -
114C LEU 3.5 3.5 + - - -
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Residues in contact with ILE 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 ASN* 5.1 2.9 - - + +
10C ILE* 1.3 81.4 - - - +
12C PHE* 1.3 74.7 + - - +
13C VAL* 3.6 6.3 + - + +
34C TYR* 3.8 27.4 - - + +
90C PHE 3.0 13.0 + - - +
91C LEU* 3.5 13.3 - - + -
92C ILE* 2.8 27.4 + - - +
113C THR* 5.4 2.2 - - - -
114C LEU* 3.3 33.2 - - + +
116C LEU* 4.3 17.5 - - + +
190C LEU* 3.8 28.0 - - + -
194C LEU* 6.3 1.1 - - + -
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Residues in contact with PHE 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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10C ILE* 4.0 9.8 + - + -
11C ILE* 1.3 74.9 - - - +
13C VAL* 1.3 59.5 + - - +
14C VAL* 4.1 7.6 - - + -
92C ILE* 3.6 10.8 - - + +
95C TYR 4.0 10.5 - - - +
96C PRO* 3.5 29.2 - - + -
102C GLY* 5.2 0.2 - - - -
105C PHE* 3.9 49.4 - + + -
106C GLU* 5.2 0.7 - - + -
112C PRO* 3.7 28.0 - - + -
114C LEU 3.0 7.8 + - - +
115C LEU* 3.3 20.3 - - + +
116C LEU 2.8 27.5 + - - +
164C TYR* 3.6 31.2 - + - -
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Residues in contact with VAL 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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11C ILE* 4.2 12.1 - - + +
12C PHE* 1.3 75.7 - - - +
14C VAL* 1.3 60.1 + - - +
21C LYS* 3.7 33.0 - - + +
24C GLN* 6.3 0.9 - - + -
25C CYS* 3.9 23.8 - - - -
91C LEU* 4.4 12.3 - - + -
92C ILE 2.7 15.0 + - - +
93C ASP* 4.3 5.6 - - - -
94C GLY* 3.4 23.4 + - - -
95C TYR 5.0 1.0 + - - +
116C LEU* 3.5 24.9 - - + +
118C VAL* 4.0 16.6 - - + -
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Residues in contact with VAL 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 PHE* 4.1 10.1 - - + -
13C VAL* 1.3 78.2 - - - +
15C GLY* 1.3 61.7 + - - +
21C LYS* 3.9 3.8 - - - -
94C GLY* 6.0 1.1 - - - -
95C TYR 5.5 1.3 - - - +
96C PRO* 5.0 11.4 - - + +
115C LEU* 3.6 39.3 - - + -
116C LEU 2.9 6.2 + - - +
117C TYR* 3.5 4.0 - - - -
118C VAL* 2.8 28.4 + - - +
153C TYR* 4.8 2.7 - - + +
157C THR* 4.1 25.8 - - + +
160C VAL* 4.9 8.7 - - + -
161C ILE* 3.7 22.2 - - + -
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Residues in contact with GLY 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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14C VAL* 1.3 81.9 - - - +
16C GLY* 1.3 63.4 + - - +
19C SER* 3.5 7.6 - - - -
21C LYS* 3.0 22.8 + - - +
97C ARG* 5.7 2.9 + - - -
117C TYR* 5.0 0.4 - - - -
118C VAL 3.5 15.0 - - - -
153C TYR* 3.4 21.3 - - - -
157C THR* 5.5 0.5 - - - +
633C AP5 4.9 0.2 + - - -
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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