Contacts of the strand formed by residues 35 - 41 (chain C) in PDB entry 6KNC
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 GLY 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C LYS 3.9 0.3 - - - +
32C THR* 2.2 48.8 + - - +
33C GLU 3.2 1.0 + - - -
34C GLU* 1.3 80.7 - - - +
36C ILE* 1.3 63.5 + - - -
37C SER* 4.0 0.4 - - - -
53C LEU 2.9 14.1 - - - -
54C PRO* 4.1 4.5 - - - -
61C TYR* 3.8 7.6 - - - -
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Residues in contact with ILE 36 (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 PHE* 5.7 0.4 - - + -
5C VAL* 4.2 9.4 - - + -
29C PHE* 4.5 23.8 - - + -
30C LYS 3.4 9.9 - - - +
31C PHE* 3.5 31.6 - - + -
35C GLY* 1.3 71.6 - - - -
37C SER* 1.3 68.1 - - - +
51C LEU* 3.4 5.8 - - + +
53C LEU* 2.9 45.0 + - + +
58C PHE* 3.6 27.1 - - + -
61C TYR* 3.3 18.8 - - + +
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Residues in contact with SER 37 (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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29C PHE* 3.7 2.9 - - - -
30C LYS* 2.8 48.6 + - - +
32C THR* 4.9 5.2 - - - +
35C GLY 3.9 1.7 + - - -
36C ILE* 1.3 76.8 - - - +
38C MET* 1.3 64.2 + - - +
39C ARG* 5.6 4.3 + - - +
50C ASP* 4.0 3.8 - - - -
51C LEU* 2.6 16.4 - - - -
52C ASN* 3.5 17.0 - - - -
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Residues in contact with MET 38 (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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20C ALA* 4.2 14.6 - - + -
24C ILE* 6.4 0.2 - - + -
27C ALA* 4.5 7.0 - - + -
28C ALA 3.4 21.8 - - - +
29C PHE* 3.5 27.6 - - + -
30C LYS* 4.5 1.3 - - - +
37C SER* 1.3 80.2 + - - +
39C ARG* 1.3 54.3 + - - +
40C ALA* 3.6 30.3 - - - -
49C ILE* 2.9 37.1 - - + +
50C ASP* 2.7 37.0 + - - -
51C LEU* 2.9 32.1 + - + -
73C MET* 5.6 0.4 - - + -
239C LEU* 5.3 0.2 - - + -
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Residues in contact with ARG 39 (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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28C ALA* 3.7 14.1 + - - +
30C LYS* 4.4 20.0 + - + +
37C SER* 5.6 3.5 + - - +
38C MET* 1.3 74.8 - - - +
40C ALA* 1.3 59.1 + - - +
48C LEU* 4.5 12.8 - - + -
49C ILE 3.2 4.3 - - - -
50C ASP* 3.5 35.6 + - + +
120C GLU* 4.2 13.7 - - - +
123C LEU 4.8 10.1 + - - +
124C GLU* 3.7 36.7 + - - +
125C LEU* 5.4 6.2 - - - +
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Residues in contact with ALA 40 (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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24C ILE* 3.9 20.2 - - + -
26C GLU 4.4 6.3 - - - +
27C ALA* 4.8 5.6 - - - -
28C ALA 4.9 1.1 - - - +
38C MET* 3.6 19.7 - - + -
39C ARG* 1.3 74.6 - - - +
41C MET* 1.3 60.2 + - - +
47C VAL 4.2 0.5 - - - +
48C LEU* 3.3 4.8 - - - +
49C ILE* 2.9 42.0 + - + +
120C GLU* 3.9 13.2 - - + -
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Residues in contact with MET 41 (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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24C ILE* 3.9 9.1 - - - +
40C ALA* 1.3 74.3 - - - +
42C ASP* 1.3 63.0 + - - +
43C PRO* 3.6 5.0 - - - +
45C ARG* 3.3 57.0 + - + +
46C VAL 4.3 0.9 - - - -
47C VAL* 3.3 31.2 - - - +
48C LEU* 3.5 28.7 - - + +
120C GLU* 2.6 31.1 + - + +
121C LEU* 4.6 13.2 - - + +
123C LEU* 3.7 27.4 - - + -
242C LEU* 5.2 7.4 - - + -
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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