Contacts of the helix formed by residues 51 - 64 (chain C) in PDB entry 3G1Q
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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47C GLN 3.4 3.9 + - - -
48C PHE 3.2 3.5 + - - -
50C LYS* 1.3 85.2 - - - +
52C PRO* 1.3 69.8 - - - +
53C LEU* 3.3 0.9 + - - +
54C GLY* 3.5 18.3 + - - -
55C PHE* 2.9 25.7 + - - +
457C TYR* 5.5 1.1 - - - -
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Residues in contact with PRO 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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48C PHE* 2.9 45.5 - - + +
49C GLY* 4.2 6.3 - - - +
51C SER* 1.3 84.0 - - - +
53C LEU* 1.3 62.9 + - - +
55C PHE* 3.9 0.7 - - - +
56C MET* 3.1 32.4 + - + +
357C LEU* 4.1 13.9 - - + -
385C LEU* 3.8 12.6 - - + -
457C TYR* 3.7 40.8 - - + -
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Residues in contact with LEU 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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51C SER* 3.3 1.0 + - - +
52C PRO* 1.3 77.9 - - - +
54C GLY* 1.3 62.2 + - - +
56C MET* 3.4 3.9 + - - +
57C GLN* 3.0 61.0 + - + +
385C LEU* 3.7 39.8 - - + +
386C LEU* 4.0 14.4 - - + -
389C HIS* 3.6 36.8 - - + +
398C ARG* 5.1 7.0 - - + +
457C TYR* 5.2 6.2 - - + +
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Residues in contact with GLY 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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51C SER* 3.5 17.4 + - - -
53C LEU* 1.3 80.4 - - - +
55C PHE* 1.3 61.5 + - - +
57C GLN* 3.5 9.5 + - - +
58C GLU* 3.0 26.0 + - - +
61C ARG* 5.3 0.9 + - - -
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Residues in contact with PHE 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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35C TYR* 4.0 15.0 - + - -
44C HIS* 3.5 36.3 - + + -
47C GLN* 3.9 38.4 - - + +
48C PHE* 3.9 26.0 - + + -
51C SER* 2.9 25.0 + - - +
52C PRO 3.9 2.2 - - - +
54C GLY* 1.3 71.4 - - - +
56C MET* 1.3 67.8 + - + +
58C GLU* 3.4 8.5 + - + +
59C CYS* 3.1 48.6 + - - -
70C ILE* 4.1 20.0 - - + -
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Residues in contact with MET 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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48C PHE* 3.9 17.5 - - + -
52C PRO* 3.1 28.0 + - + +
53C LEU* 3.9 3.1 - - - +
55C PHE* 1.3 85.4 - - + +
57C GLN* 1.3 61.6 + - - +
59C CYS* 3.3 7.8 + - - +
60C LYS* 3.1 23.4 + - - +
68C PHE* 3.8 5.8 - - + -
79C ILE* 3.9 26.0 - - + -
357C LEU* 6.0 0.2 - - + -
358C MET* 3.8 24.7 - - + -
383C SER* 3.4 26.2 - - - +
385C LEU* 4.2 13.5 - - + -
386C LEU* 3.8 30.2 - - + +
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Residues in contact with GLN 57 (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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53C LEU* 3.0 45.1 + - + +
54C GLY* 3.9 6.7 - - - +
56C MET* 1.3 76.5 - - - +
58C GLU* 1.3 58.3 + - - +
60C LYS* 3.4 9.8 + - + +
61C ARG* 3.0 49.9 + - - +
386C LEU* 4.0 16.1 - - + +
389C HIS* 3.6 25.7 + - - +
391C GLU* 5.0 7.1 + - - -
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Residues in contact with GLU 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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35C TYR* 4.2 7.4 - - - +
54C GLY 3.0 18.2 + - - +
55C PHE* 3.5 9.9 - - + +
57C GLN* 1.3 74.4 - - - +
59C CYS* 1.3 65.8 + - - +
61C ARG* 2.8 39.5 + - - +
62C GLN* 2.6 68.7 + - - +
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Residues in contact with CYS 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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35C TYR* 3.6 38.1 - - + -
55C PHE* 3.1 50.0 + - - -
56C MET 3.5 3.4 - - - +
58C GLU* 1.3 74.6 - - - +
60C LYS* 1.3 58.0 + - - +
62C GLN* 3.9 0.2 - - - -
63C LEU* 2.9 38.1 + - + +
68C PHE* 3.5 30.7 - - + -
70C ILE* 4.2 2.0 - - - -
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Residues in contact with LYS 60 (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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56C MET 3.1 11.7 + - - +
57C GLN* 3.6 11.4 - - + +
59C CYS* 1.3 77.6 - - - +
61C ARG* 1.3 62.9 + - - +
64C LYS* 3.0 18.7 + - - -
65C SER 3.2 33.5 + - - +
66C GLY* 3.9 11.9 - - - +
68C PHE* 4.2 10.3 - - + -
81C GLY 2.9 29.1 + - - +
82C ASP* 4.8 0.8 - - - +
83C PRO* 4.7 1.6 - - - +
386C LEU* 4.9 16.6 + - + +
390C ASP* 3.3 27.1 + - - +
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Residues in contact with ARG 61 (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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54C GLY 5.3 0.6 + - - -
57C GLN* 3.0 37.6 + - - +
58C GLU* 2.8 50.3 + - - +
59C CYS 3.2 0.2 - - - -
60C LYS* 1.3 73.1 - - - +
62C GLN* 1.3 66.4 + - + +
64C LYS* 3.1 20.7 + - - +
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Residues in contact with GLN 62 (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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35C TYR* 3.3 33.5 + - + -
58C GLU* 2.6 44.0 + - - +
59C CYS 4.1 1.6 - - - +
61C ARG* 1.3 79.0 - - + +
63C LEU* 1.3 65.3 + - + +
64C LYS* 3.1 7.4 + - - +
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Residues in contact with LEU 63 (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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33C PRO* 3.8 33.7 - - + +
34C VAL 3.8 15.3 - - - +
35C TYR* 3.9 36.3 - - + +
36C PRO* 4.7 4.9 - - + -
59C CYS 2.9 18.3 + - - +
62C GLN* 1.3 79.1 - - + +
64C LYS* 1.3 71.0 + - - +
65C SER* 3.3 10.6 + - - +
68C PHE* 3.6 29.6 - - + -
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Residues in contact with LYS 64 (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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60C LYS 3.0 10.6 + - - -
61C ARG 3.1 13.0 + - - +
62C GLN 3.1 6.9 - - - +
63C LEU* 1.3 80.8 - - - +
65C SER* 1.3 58.9 + - - +
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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