Contacts of the helix formed by residues 51 - 63 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN 3.2 5.3 + - - -
48B PHE 3.5 1.6 - - - -
50B LYS* 1.3 83.3 - - - +
52B PRO* 1.3 70.1 - - - +
53B LEU 3.3 2.0 - - - -
54B GLY* 3.8 11.8 - - - -
55B PHE* 2.9 28.2 + - - +
457B TYR* 5.3 4.5 - - - -
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Residues in contact with PRO 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.0 47.5 - - + +
49B GLY* 3.9 9.2 - - - +
50B LYS 4.0 0.2 - - - -
51B SER* 1.3 85.2 - - - +
53B LEU* 1.3 62.7 + - - +
55B PHE* 3.8 0.5 - - - +
56B MET* 3.1 33.8 + - + +
357B LEU* 3.9 16.2 - - + -
385B LEU* 3.9 9.9 - - + -
457B TYR* 3.7 37.5 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER* 3.3 1.2 - - - -
52B PRO* 1.3 80.5 - - - +
54B GLY* 1.3 68.3 + - - +
56B MET* 4.0 2.4 - - + -
57B GLN* 3.0 57.4 + - + +
385B LEU* 3.6 44.1 - - + +
386B LEU* 4.4 6.1 - - + -
389B HIS* 3.8 36.6 - - + +
398B ARG* 4.6 10.1 - - - +
457B TYR* 4.5 14.1 - - + +
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER* 3.4 16.7 + - - -
53B LEU* 1.3 80.0 - - - +
55B PHE* 1.3 63.1 + - - +
57B GLN* 3.6 7.8 + - - +
58B GLU* 3.1 25.1 + - - +
61B ARG* 5.3 0.7 + - - -
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 4.1 16.2 - + - -
44B HIS* 3.5 36.8 - + + -
47B GLN* 3.8 34.8 - - + +
48B PHE* 3.8 26.5 - + + -
51B SER* 2.9 22.2 + - - +
52B PRO 3.8 1.6 - - - +
54B GLY* 1.3 77.1 - - - +
56B MET* 1.3 66.9 + - + +
58B GLU* 3.4 7.7 + - + +
59B CYS* 3.1 47.0 + - - -
70B ILE* 3.9 23.3 - - + -
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Residues in contact with MET 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.8 19.5 - - + -
52B PRO* 3.1 29.1 + - + +
53B LEU* 4.2 3.1 - - - +
55B PHE* 1.3 84.7 - - + +
57B GLN* 1.3 62.9 + - - +
59B CYS* 3.4 7.9 + - - +
60B LYS* 3.1 23.6 + - - +
68B PHE* 3.8 5.3 - - + -
79B ILE* 3.9 23.6 - - + -
358B MET* 3.6 27.1 - - + -
383B SER* 3.6 24.0 - - - +
385B LEU* 4.1 14.6 - - + -
386B LEU* 4.0 28.0 - - + +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.0 47.4 + - + +
54B GLY* 4.0 7.0 - - - +
56B MET* 1.3 77.2 - - - +
58B GLU* 1.3 56.2 - - - +
60B LYS* 3.4 4.9 + - + +
61B ARG* 3.0 36.9 + - - +
386B LEU* 4.1 12.9 - - + +
389B HIS* 3.6 30.9 + - - +
391B GLU* 4.9 8.9 + - - -
397B PRO* 5.6 1.4 - - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.9 14.8 - - - +
54B GLY 3.1 19.0 + - - +
55B PHE* 3.8 7.2 - - + +
57B GLN* 1.3 74.9 - - - +
59B CYS* 1.3 66.4 + - - +
61B ARG* 2.5 43.7 + - - +
62B GLN* 2.7 65.5 + - - +
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Residues in contact with CYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.7 33.2 - - + -
55B PHE* 3.1 52.2 + - - -
56B MET* 3.5 4.5 - - - +
58B GLU* 1.3 76.1 - - - +
60B LYS* 1.3 55.8 + - - +
63B LEU* 2.9 38.6 + - + +
68B PHE* 3.4 31.9 - - + -
70B ILE* 4.0 2.2 - - - -
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B MET 3.1 16.2 + - - +
57B GLN* 3.7 6.5 - - - +
59B CYS* 1.3 75.4 - - - +
61B ARG* 1.3 63.4 + - - +
64B LYS* 3.1 18.9 + - - -
65B SER 3.2 32.4 + - - +
66B GLY* 4.0 12.3 - - - +
68B PHE* 4.1 7.2 - - + -
81B GLY 2.6 29.6 + - - +
82B ASP* 4.6 0.8 - - - +
83B PRO* 4.4 0.4 - - - +
386B LEU* 4.4 20.3 - - + +
390B ASP* 2.9 35.8 + - - +
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLY 5.3 0.8 + - - -
57B GLN* 3.0 19.6 + - - +
58B GLU* 2.5 48.5 + - - +
60B LYS* 1.3 76.4 - - - +
62B GLN* 1.3 60.7 + - - +
64B LYS* 3.3 22.3 + - - +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 2.7 39.6 + - + -
36B PRO* 4.9 10.2 - - - +
58B GLU* 2.7 45.5 + - - +
59B CYS 4.1 1.8 - - - +
61B ARG* 1.3 73.0 - - - +
63B LEU* 1.3 63.5 + - + +
64B LYS* 3.2 12.1 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 3.9 27.6 - - + +
34B VAL 4.0 14.1 - - - +
35B TYR* 3.7 41.7 - - + +
36B PRO* 4.6 5.2 - - + -
59B CYS 2.9 19.9 + - - +
62B GLN* 1.3 81.8 - - + +
64B LYS* 1.3 68.8 + - - +
65B SER* 3.2 10.9 + - - +
68B PHE* 3.6 30.1 - - + -
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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