Contacts of the strand formed by residues 21 - 30 (chain C) in PDB entry 4K71
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 ASN 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573A LYS* 3.3 12.3 + - - +
11C SER* 4.1 3.0 - - - -
12C ARG* 3.4 2.1 + - - +
13C HIS* 2.9 57.9 + - - +
14C PRO 3.8 10.3 + - - -
15C ALA* 3.9 11.5 - - - +
16C GLU 4.9 1.0 - - - +
19C LYS 4.2 5.3 + - - +
20C SER* 1.3 76.2 + - - +
22C PHE* 1.3 86.2 + - - +
69C GLU* 3.4 3.6 - - - +
70C PHE* 2.8 42.3 + - + +
72C PRO* 4.2 3.7 - - + +
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Residues in contact with PHE 22 (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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503A ASN* 5.4 0.4 - - - -
504A ALA* 3.9 14.4 - - + -
505A GLY* 3.6 31.6 - - - -
573A LYS* 3.8 23.6 - - + -
230B SER* 4.8 2.5 - - - +
11C SER* 3.3 4.0 - - - -
12C ARG* 2.9 68.2 + - + -
13C HIS* 5.6 1.8 - + - -
21C ASN* 1.3 85.8 + - - +
23C LEU* 1.3 58.7 + - - +
24C ASN* 4.4 8.7 - - - +
50C GLU* 6.0 1.1 - - - -
67C TYR* 4.2 18.2 - + - -
68C THR 3.4 7.4 - - - -
69C GLU* 3.7 33.4 - - + -
70C PHE* 3.4 6.5 - - - -
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Residues in contact with LEU 23 (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 VAL* 4.0 14.8 - - + -
10C TYR 4.0 5.8 - - - +
22C PHE* 1.3 73.3 - - - +
24C ASN* 1.3 64.8 + - - +
39C LEU* 4.3 25.2 - - + +
67C TYR* 3.2 6.4 - - - +
68C THR* 2.8 39.3 + - + +
70C PHE* 3.3 24.9 - - + -
78C TYR* 3.6 36.1 - - + -
79C ALA 4.9 3.6 - - - +
95C TRP* 3.7 39.7 - - + +
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Residues in contact with ASN 24 (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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229B ASN* 3.0 33.5 + - - +
230B SER* 4.6 3.8 + - - -
8C GLN 3.8 0.7 - - - +
9C VAL* 3.3 7.2 - - - +
10C TYR* 2.8 62.6 + - + +
12C ARG* 3.9 11.9 - - - +
22C PHE* 4.4 8.7 - - - +
23C LEU* 1.3 76.9 - - - +
25C CYS* 1.3 60.5 + - - +
26C TYR 4.1 0.2 - - - -
39C LEU* 5.0 0.7 - - - -
65C LEU* 4.0 16.3 - - + +
66C TYR 3.4 3.4 - - - -
67C TYR* 3.4 20.1 - - - +
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Residues in contact with CYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.8 18.2 - - - -
8C GLN 3.4 4.9 - - - -
9C VAL* 4.7 0.9 - - + -
23C LEU 4.4 0.2 - - - -
24C ASN* 1.3 71.3 - - - +
26C TYR* 1.3 59.9 + - - +
27C VAL* 3.9 12.7 + - - +
37C VAL* 4.3 0.4 - - - -
39C LEU* 3.7 16.5 - - + +
64C LEU 3.8 1.4 - - - +
65C LEU* 3.5 2.8 - - - -
66C TYR* 2.7 44.8 + - + +
80C CYS* 2.0 50.7 - - + -
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Residues in contact with TYR 26 (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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226B PHE 3.9 12.6 - - - -
227B GLY* 4.1 3.8 - - - -
228B PRO* 3.5 34.8 - - + +
6C LYS 3.7 1.0 - - - +
7C ILE* 3.5 2.4 - - - -
8C GLN* 2.9 51.7 + - - +
10C TYR* 3.5 23.1 - - + +
24C ASN 4.1 0.6 - - - -
25C CYS* 1.3 71.8 - - - +
27C VAL* 1.3 59.7 + - - +
28C SER* 3.6 26.3 - - - -
57C SER* 5.4 0.7 + - - -
63C TYR* 3.6 45.5 - + + +
64C LEU 3.6 13.2 - - - -
65C LEU* 3.7 7.0 - - + -
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Residues in contact with VAL 27 (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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5C PRO* 3.4 33.2 - - + -
6C LYS 3.2 6.3 - - - +
7C ILE* 4.4 4.9 - - + -
25C CYS* 4.0 15.5 - - - +
26C TYR* 1.3 75.3 - - - +
28C SER* 1.3 60.6 - - - +
30C PHE* 3.6 5.7 - - + -
35C ILE* 3.7 17.0 - - + -
37C VAL* 4.2 15.3 - - + -
63C TYR* 3.2 3.6 - - - +
64C LEU* 2.8 41.8 + - + +
66C TYR* 5.7 0.7 - - + -
82C VAL* 3.9 27.1 - - + -
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Residues in contact with SER 28 (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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5C PRO* 3.4 1.4 - - - +
6C LYS* 2.8 51.3 + - - +
8C GLN* 5.1 2.9 + - - -
26C TYR* 3.6 26.5 - - - -
27C VAL* 1.3 75.0 - - - +
29C GLY* 1.3 64.7 + - - +
30C PHE* 3.3 5.4 + - - -
57C SER* 6.1 0.4 - - - -
62C PHE 3.4 6.7 - - - -
63C TYR* 3.6 14.4 - - - -
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Residues in contact with GLY 29 (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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3C ARG* 3.2 22.5 - - - +
4C THR 3.5 10.3 - - - +
6C LYS* 5.4 7.6 - - - +
28C SER* 1.3 75.7 - - - +
30C PHE* 1.3 58.7 + - - +
57C SER* 6.0 0.2 + - - -
61C SER* 3.5 24.1 + - - -
62C PHE 2.9 7.1 + - - -
63C TYR* 4.6 0.2 - - - +
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Residues in contact with PHE 30 (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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3C ARG* 3.4 14.1 - - - +
5C PRO* 3.8 22.7 - - + -
27C VAL* 3.6 21.1 - - + -
28C SER 3.9 4.9 - - - -
29C GLY* 1.3 79.3 - - - +
31C HIS* 1.3 62.8 + - - +
32C PRO 3.3 19.5 - - - -
33C SER 3.6 21.8 - - - -
35C ILE* 3.5 40.4 - - + -
54C LEU* 3.9 16.4 - - + -
61C SER* 3.7 1.5 - - - -
62C PHE* 2.7 62.8 + - + +
63C TYR* 4.0 1.3 - - - -
64C LEU* 4.5 3.1 - - + -
84C HIS* 3.8 10.5 - - - +
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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