Contacts of the helix formed by residues 57 - 68 (chain B) in PDB entry 4QGC
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 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA 5.7 0.5 - - - -
55B SER 3.3 0.9 - - - +
56B ARG* 1.3 83.5 - - - +
58B VAL* 1.3 64.1 + - - +
59B GLU* 4.2 7.9 + - - +
60B THR* 2.8 31.4 + - - -
61B LEU* 3.0 21.5 + - - +
90B ASN* 4.4 4.5 - - - +
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Residues in contact with VAL 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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56B ARG 3.6 0.2 + - - -
57B SER* 1.3 72.6 - - - +
59B GLU* 1.3 57.7 + - - +
61B LEU* 3.5 7.9 + - - +
62B LYS* 3.0 56.6 + - - +
90B ASN* 3.9 34.5 - - + +
93B THR* 4.0 24.7 - - + -
94B ALA* 4.1 7.9 - - - -
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Residues in contact with GLU 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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57B SER* 3.2 7.8 + - - +
58B VAL* 1.3 80.7 - - - +
60B THR* 1.3 64.3 + - - +
62B LYS* 3.4 11.8 + - - +
63B GLU* 3.3 26.6 + - + +
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Residues in contact with THR 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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54B ALA 3.9 8.9 + - - +
55B SER* 3.8 26.7 - - - -
57B SER* 2.8 23.9 + - - -
59B GLU* 1.3 78.6 + - - +
61B LEU* 1.3 62.4 + - - +
63B GLU* 3.2 7.8 + - - +
64B MET* 2.9 40.4 + - + +
371B PRO* 4.6 9.6 - - + -
372B LEU* 5.5 6.1 - - + -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.7 27.4 - - + -
55B SER 3.2 20.0 - - - +
56B ARG* 3.3 21.8 - - - +
57B SER 3.0 11.7 + - - +
58B VAL 3.8 0.2 - - - +
59B GLU 3.3 0.2 - - - -
60B THR* 1.3 77.1 - - - +
62B LYS* 1.3 56.4 + - - +
64B MET* 3.2 7.4 + - - +
65B ILE* 2.9 34.8 + - + +
69B MET* 4.0 15.4 - - + +
87B THR 4.8 0.2 - - - +
90B ASN* 3.6 9.2 - - + +
91B VAL* 3.5 42.6 - - + +
94B ALA* 3.7 15.3 - - + -
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Residues in contact with LYS 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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58B VAL* 3.0 44.1 + - + +
59B GLU* 3.5 9.4 - - - +
61B LEU* 1.3 77.7 - - - +
63B GLU* 1.3 60.4 + - + +
65B ILE* 3.5 3.3 + - - +
66B LYS* 3.1 34.1 + - + +
93B THR* 5.0 1.1 - - - -
94B ALA* 3.8 14.3 - - + +
97B SER* 3.4 33.4 - - - +
98B PHE* 3.6 16.0 - - + -
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Residues in contact with GLU 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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59B GLU* 3.3 18.3 + - + +
60B THR* 3.2 10.4 + - - +
62B LYS* 1.3 76.2 - - + +
64B MET* 1.3 62.0 + - - +
66B LYS* 3.4 33.8 + - - +
67B SER* 2.9 32.7 + - - -
372B LEU* 3.7 26.0 - - + -
376B ARG* 4.2 13.5 + - - -
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Residues in contact with MET 64 (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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49B CYS* 3.8 24.5 - - + -
51B ILE* 4.2 7.4 - - + -
55B SER* 3.6 26.9 - - - +
60B THR* 2.9 30.9 + - + +
61B LEU* 3.2 8.9 + - - +
63B GLU* 1.3 73.0 - - - +
65B ILE* 1.3 60.4 + - - +
67B SER* 3.2 4.8 + - - -
68B GLY 3.0 10.0 + - - -
69B MET* 2.9 39.8 + - + +
365B THR* 4.0 13.5 - - + -
371B PRO* 4.8 4.3 - - - +
372B LEU* 4.1 15.9 - - + -
375B VAL* 3.7 29.9 - - + +
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Residues in contact with ILE 65 (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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61B LEU* 2.9 21.7 + - + +
62B LYS 3.6 4.7 - - - +
63B GLU 3.3 0.2 - - - -
64B MET* 1.3 76.3 - - - +
66B LYS* 1.3 61.4 + - + +
68B GLY* 3.2 13.3 + - - -
69B MET* 3.7 29.0 + - + +
91B VAL* 4.7 1.1 - - + +
94B ALA* 3.9 12.3 - - + +
95B THR* 3.6 42.4 - - - +
98B PHE* 4.1 16.8 - - + -
106B ARG* 4.9 19.0 - - + +
108B VAL* 3.8 20.0 - - + -
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Residues in contact with LYS 66 (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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62B LYS* 3.1 18.3 + - + +
63B GLU* 3.6 37.0 + - - +
64B MET 3.3 0.2 - - - -
65B ILE* 1.3 77.4 - - + +
67B SER* 1.3 59.7 + - - +
68B GLY* 3.6 0.3 + - - -
98B PHE* 3.7 27.8 - - + -
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 2.9 22.4 + - - -
64B MET 3.6 5.4 - - - -
65B ILE 3.1 0.6 - - - -
66B LYS* 1.3 78.5 - - - +
68B GLY* 1.3 56.0 + - - +
69B MET 3.9 0.2 - - - -
372B LEU* 3.4 7.2 - - - +
375B VAL* 3.9 15.0 - - - +
376B ARG* 3.1 45.5 + - - +
379B HIS* 3.8 27.4 + - - +
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 2.9 31.1 + - - -
47B ILE* 3.5 12.2 - - - +
64B MET 3.0 0.8 + - - -
65B ILE 3.2 8.7 + - - -
66B LYS 3.3 0.6 - - - -
67B SER* 1.3 81.8 - - - +
69B MET* 1.3 67.2 + - - +
70B ASN* 3.3 12.9 + - - +
375B VAL* 4.4 0.7 - - - -
379B HIS* 5.1 0.4 - - - -
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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