Contacts of the helix formed by residues 43 - 53 (chain C) in PDB entry 6T2C
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 PRO 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B ALA 4.0 15.7 - - - +
516B GLY* 4.4 6.7 - - - +
42C ASN* 1.3 84.4 - - + +
44C ALA* 1.3 64.2 + - + +
46C ARG* 3.6 7.3 - - + +
47C MET* 2.9 29.1 + - - +
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Residues in contact with ALA 44 (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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514B VAL* 3.7 25.4 - - + +
515B ALA* 3.8 11.2 + - - +
516B GLY* 4.8 0.2 - - - -
558B THR* 5.5 0.2 - - - +
42C ASN* 3.4 1.1 - - + -
43C PRO* 1.3 81.6 - - + +
45C LEU* 1.3 64.2 + - + +
47C MET* 3.3 5.7 + - - +
48C LYS* 2.9 44.3 + - - +
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Residues in contact with LEU 45 (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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465A LEU* 3.8 30.7 - - + -
567A LYS* 3.4 38.8 - - + +
571A LYS* 3.8 36.1 - - + -
574A MET* 5.1 8.5 - - + -
575A GLU* 5.4 1.8 - - - +
42C ASN* 3.9 21.9 + - + +
43C PRO 3.4 0.2 - - - -
44C ALA* 1.3 84.7 - - + +
46C ARG* 1.3 58.1 + - - +
48C LYS* 3.2 15.2 + - + +
49C TRP* 3.0 34.9 + - + +
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Residues in contact with ARG 46 (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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671B ASN* 3.7 34.3 + - - +
42C ASN 3.2 20.6 + - - +
43C PRO* 3.6 7.9 - - + +
44C ALA 3.2 0.4 - - - -
45C LEU* 1.3 79.1 - - - +
47C MET* 1.3 57.4 + - - +
49C TRP* 3.4 32.1 + - + +
50C MET* 2.9 40.4 + - + +
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Residues in contact with MET 47 (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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514B VAL* 5.7 0.9 - - + -
516B GLY* 3.4 35.4 - - - +
517B ASN 3.8 17.5 - - - +
558B THR* 4.6 7.2 - - + -
559B TYR* 3.8 24.9 - - + +
666B TRP* 4.7 4.9 - - + -
668B PRO* 4.2 10.1 - - + -
43C PRO 2.9 16.9 + - - +
44C ALA* 3.3 5.4 + - - +
46C ARG* 1.3 76.1 - - - +
48C LYS* 1.3 58.0 + - - +
50C MET* 3.8 26.5 - - + -
51C MET* 2.9 50.3 + - + +
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Residues in contact with LYS 48 (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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466A ASN* 4.5 6.0 - - - +
574A MET* 3.7 31.6 - - + +
575A GLU* 5.8 2.0 + - - -
513B GLY* 6.0 0.8 - - - -
514B VAL* 4.3 13.3 + - - +
554B ASP* 3.6 26.0 + - - -
557B TYR* 4.3 19.0 + - + +
558B THR* 3.7 26.7 - - + -
560B ARG* 4.2 10.1 + - - +
44C ALA* 2.9 31.6 + - - +
45C LEU* 3.2 14.2 + - + +
47C MET* 1.3 78.5 - - - +
49C TRP* 1.3 59.5 + - - +
51C MET* 5.0 0.9 - - - -
52C ALA* 3.6 16.8 + - - +
33V C 5.8 0.2 - - - +
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Residues in contact with TRP 49 (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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465A LEU* 5.4 1.6 - - + +
466A ASN* 4.8 8.3 - - - +
469A CYS* 3.7 50.8 - - + -
470A THR* 5.3 3.9 + - - +
567A LYS* 6.1 2.2 - - - +
45C LEU* 3.0 31.5 + - + +
46C ARG* 3.4 43.4 - - + +
48C LYS* 1.3 76.5 - - - +
50C MET* 1.3 68.5 + - + +
52C ALA* 3.7 15.0 + - + +
53C MET* 3.6 42.2 - - + +
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Residues in contact with MET 50 (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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666B TRP* 6.0 0.2 - - + -
668B PRO* 3.7 27.6 - - + -
669B LYS* 3.6 41.7 - - + +
46C ARG* 2.9 26.1 + - + +
47C MET* 3.8 28.7 - - + +
49C TRP* 1.3 87.3 - - + +
51C MET* 1.3 63.2 + - - +
52C ALA 3.2 1.9 + - - -
53C MET* 3.5 19.2 + - + +
56C PRO* 3.4 28.0 - - + +
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Residues in contact with MET 51 (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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519B GLU* 5.2 2.5 - - - +
558B THR 3.6 19.3 - - - +
559B TYR* 4.0 41.3 - - + +
560B ARG* 3.7 10.8 + - + +
571B ARG* 2.6 37.2 + - - +
572B ARG* 5.0 2.7 - - - +
666B TRP* 4.4 12.8 - - + -
47C MET* 2.9 40.3 + - + +
48C LYS* 4.4 0.9 - - - +
50C MET* 1.3 74.8 - - - +
52C ALA* 1.3 57.5 + - - +
53C MET 3.3 2.5 - - - +
56C PRO* 4.0 20.5 - - - +
93C PRO* 4.2 22.9 - - + -
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Residues in contact with ALA 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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466A ASN* 4.4 9.2 - - - +
470A THR* 5.0 7.4 - - - +
560B ARG* 4.1 12.0 - - - +
571B ARG* 3.4 1.6 + - - +
48C LYS 3.6 13.7 + - - +
49C TRP* 3.8 10.8 - - - +
50C MET 3.2 1.0 - - - -
51C MET* 1.3 76.4 - - - +
53C MET* 1.3 63.7 + - - +
30V C 3.4 14.8 + - - +
31V U 3.4 46.3 + - - +
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Residues in contact with MET 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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469A CYS 4.6 8.1 - - - +
470A THR* 5.0 12.1 - - - +
571B ARG* 3.8 5.7 + - - -
669B LYS* 6.0 6.7 - - - -
49C TRP* 3.6 44.0 - - + +
50C MET* 3.5 15.9 + - + +
51C MET 3.3 12.1 - - - +
52C ALA* 1.3 83.2 - - + +
54C LYS* 1.3 66.1 + - - +
55C TYR 3.5 6.0 + - - +
56C PRO* 4.3 2.8 - - - +
30V C 3.3 37.2 - - + +
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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