Contacts of the strand formed by residues 51 - 59 (chain C) in PDB entry 1CVJ
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 SER 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C LEU* 5.4 1.7 - - - +
19C HIS 4.7 2.4 + - - -
20C PRO* 3.5 36.7 + - - +
22C VAL 5.2 2.2 + - - -
42C VAL* 3.8 20.7 - - - +
43C CYS 3.7 5.8 - - - -
44C ARG* 3.9 8.1 - - - -
49C ARG 3.2 3.8 + - - -
50C ARG* 1.3 86.3 - - - +
52C LEU* 1.3 57.3 + - - +
53C GLY* 3.1 19.8 + - - -
54C TYR 4.6 0.2 + - - -
25D ALA* 4.7 4.6 - - - +
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Residues in contact with LEU 52 (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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43C CYS* 2.7 34.8 + - + +
44C ARG 3.7 10.1 - - - +
45C ASP* 3.4 26.9 - - + +
50C ARG* 3.6 4.0 - - + +
51C SER* 1.3 71.9 - - - +
53C GLY* 1.3 60.9 + - - +
54C TYR* 3.4 20.9 + - + -
4O A 4.9 11.5 + - - +
5O A 3.6 50.7 - - + +
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Residues in contact with GLY 53 (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 ASP* 3.1 10.6 + - - -
18C LEU* 2.9 44.3 + - - -
19C HIS 5.7 0.4 - - - -
20C PRO* 5.8 1.1 - - - -
51C SER* 3.1 15.9 + - - -
52C LEU* 1.3 76.3 - - - +
54C TYR* 1.3 58.7 + - - +
4O A 4.8 3.2 + - - -
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Residues in contact with TYR 54 (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 TYR* 3.1 43.1 - + + +
15C VAL 3.3 5.6 - - - -
16C GLY* 3.6 6.3 - - - -
18C LEU* 3.9 5.5 - - - +
42C VAL* 3.8 5.2 - - - +
43C CYS* 3.2 48.6 + - + +
51C SER* 4.6 0.4 + - - -
52C LEU* 3.6 27.1 - - + -
53C GLY* 1.3 79.8 - - - +
55C ALA* 1.3 66.0 + - - +
56C TYR* 4.1 10.1 - + - -
4O A 3.7 31.3 + - - +
5O A 2.6 30.8 + - - +
6O A 2.6 21.0 + - - -
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Residues in contact with ALA 55 (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 TYR* 3.4 7.4 - - - -
15C VAL* 2.7 45.7 + - + -
18C LEU* 3.9 2.5 - - + -
27C LEU* 3.3 33.7 - - + -
41C ARG 3.1 15.3 - - - +
42C VAL* 3.8 5.2 - - + -
43C CYS* 4.6 1.6 - - - +
54C TYR* 1.3 80.0 - - - +
56C TYR* 1.3 66.1 + - - +
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Residues in contact with TYR 56 (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 3.3 10.3 - - - +
14C TYR* 4.8 2.9 - + - -
40C ILE* 3.5 1.0 - - - +
41C ARG* 2.7 36.0 + - - +
43C CYS* 3.6 30.1 - - - -
54C TYR* 4.1 9.9 - + - -
55C ALA* 1.3 77.4 - - - +
57C VAL* 1.3 64.9 + - - +
58C ASN* 4.2 1.5 - - - +
87C SER* 3.8 22.0 - - - -
89C ARG* 3.7 11.5 + - + +
4O A 4.1 14.3 + + - -
6O A 2.4 103.6 + + + +
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Residues in contact with VAL 57 (chain C).
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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11C ALA 3.8 1.0 - - - +
13C LEU* 2.8 40.0 + - + +
15C VAL* 3.8 21.5 - - + -
27C LEU* 4.7 3.4 - - + -
31C PHE* 4.1 26.9 - - + -
37C ILE* 4.4 2.9 - - + -
40C ILE* 3.1 39.3 - - + -
56C TYR* 1.3 78.8 - - - +
58C ASN* 1.3 62.9 + - - +
59C PHE* 3.6 28.4 + - + -
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Residues in contact with ASN 58 (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 ALA* 3.6 4.7 - - + +
12C SER* 2.3 45.6 + - - +
37C ILE* 3.3 7.5 - - - +
38C LEU* 2.7 35.4 + - + -
39C SER* 2.9 28.8 + - - +
56C TYR* 4.4 1.6 - - - +
57C VAL* 1.3 79.2 + - - +
59C PHE* 1.3 65.1 + - - +
6O A 2.8 33.8 - - - +
993O A 3.7 9.5 - - + -
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Residues in contact with PHE 59 (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 ALA* 3.2 18.7 + - - +
13C LEU* 4.2 7.4 - - + -
31C PHE* 3.5 29.4 - - + -
34C ALA* 3.4 27.8 - - + -
35C GLY 3.5 23.1 - - - -
36C PRO 3.8 4.5 - - - -
37C ILE* 4.2 7.0 - - + +
38C LEU* 3.9 12.9 - - - +
57C VAL* 3.6 23.8 - - + -
58C ASN* 1.3 80.2 - - - +
60C GLN* 1.3 63.5 + - - +
61C GLN 3.9 16.4 - - - +
64C ASP* 3.5 17.9 - - + -
65C ALA* 3.7 27.8 - - + +
68C ALA* 3.8 10.8 - - + -
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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