Contacts of the helix formed by residues 58 - 70 (chain A) in PDB entry 1QFM
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLN 4.2 3.1 - - - +
57A CSX 1.3 88.7 - - + +
59A ILE* 1.3 63.5 + - - +
60A ARG 3.3 0.2 - - - -
61A GLY* 3.1 14.3 + - - +
62A LEU* 3.1 24.9 + - + +
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU 5.6 1.1 - - - +
57A CSX 3.9 19.7 - - + +
58A PRO* 1.3 78.2 - - - +
60A ARG* 1.3 68.0 + - + +
62A LEU* 3.2 7.0 + - + +
63A TYR* 2.9 24.4 + - + +
495A MET* 5.0 6.5 - - + -
697A PHE 4.8 0.9 - - - +
698A ALA* 4.2 19.1 - - + +
701A ALA* 3.5 34.1 - - + -
702A ARG* 4.8 4.5 - - + +
706A ILE 4.9 4.3 - - - +
708A TRP* 3.5 50.9 - - + +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.5 28.0 - - - +
55A GLU* 3.9 31.9 + - - +
57A CSX 3.5 5.9 + - - +
58A PRO 3.2 1.2 + - - -
59A ILE* 1.3 82.6 - - - +
61A GLY* 1.3 58.3 + - - +
63A TYR* 3.7 3.9 - - - +
64A LYS* 2.8 46.3 + - - +
691A GLU* 2.8 46.7 + - - +
694A SER* 3.8 18.5 - - - +
695A ASP* 2.7 32.6 + - - +
698A ALA* 3.6 12.1 - - + -
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Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A CSX 4.7 0.8 + - - -
58A PRO 3.1 8.3 + - - -
60A ARG* 1.3 76.4 - - - +
62A LEU* 1.3 60.6 + - - +
64A LYS* 3.9 6.3 - - - +
65A GLU* 2.9 42.3 + - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PRO* 3.1 27.6 + - + +
59A ILE* 3.6 13.2 - - - +
61A GLY* 1.3 75.6 - - - +
63A TYR* 1.3 63.8 + - - +
65A GLU* 3.6 18.3 - - - +
66A ARG* 3.1 24.1 + - - +
708A TRP* 3.7 53.7 - - + +
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 2.9 20.3 + - + +
60A ARG* 3.7 6.1 - - - +
62A LEU* 1.3 76.9 - - - +
64A LYS* 1.3 59.7 + - - +
66A ARG* 3.2 2.9 + - - +
67A MET* 2.8 34.5 + - + +
487A SER* 2.8 42.1 + - - -
490A ILE* 3.4 30.7 - - + -
491A PHE 4.6 2.0 - - - -
495A MET* 4.4 6.5 - - - -
693A VAL* 3.8 26.0 - - + -
694A SER* 3.7 18.4 - - - +
697A PHE* 3.2 39.0 - + + -
698A ALA 5.6 0.9 - - - +
708A TRP* 3.7 17.6 - + + -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG* 2.8 35.4 + - - +
61A GLY* 3.9 7.6 - - - +
63A TYR* 1.3 77.2 - - - +
65A GLU* 1.3 62.6 + - + +
67A MET* 3.4 3.6 + - - +
68A THR* 2.8 34.9 + - - +
690A ILE* 4.0 13.5 - - + -
691A GLU* 2.8 32.4 + - - +
694A SER* 3.3 20.4 - - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY* 2.9 31.2 + - - +
62A LEU* 3.6 18.9 + - - +
64A LYS* 1.3 77.0 - - + +
66A ARG* 1.3 58.3 + - - +
68A THR* 3.3 5.4 + - - -
69A GLU* 3.0 44.0 + - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU 3.1 13.4 + - - +
63A TYR 3.7 3.1 - - - +
65A GLU* 1.3 77.7 - - - +
67A MET* 1.3 60.0 + - - +
69A GLU* 3.0 26.2 + - - +
70A LEU* 2.8 70.7 + - + +
429A GLY* 3.8 23.2 + - - -
490A ILE* 3.9 5.6 - - + -
494A HIS* 2.9 47.3 + - + +
708A TRP* 3.8 13.9 - - + -
710A PRO* 5.7 0.7 - - - -
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Residues in contact with MET 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 2.8 28.9 + - + +
64A LYS* 3.7 6.1 - - - +
66A ARG* 1.3 71.2 - - - +
68A THR* 1.3 56.1 + - - +
71A TYR* 2.7 74.0 + - + +
486A VAL* 3.9 16.2 - - + -
487A SER* 4.0 24.0 - - - +
490A ILE* 3.5 13.4 - - + +
689A VAL* 4.9 10.1 - - + -
690A ILE* 4.1 20.4 - - + -
693A VAL* 3.9 26.7 - - + -
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS* 2.8 29.2 + - - +
65A GLU* 3.6 6.7 - - - -
67A MET* 1.3 76.5 - - - +
69A GLU* 1.3 61.4 + - + +
72A ASP* 3.3 22.0 + - - +
94A LEU* 3.8 24.6 - - + +
690A ILE* 3.8 26.7 - - + +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 3.0 28.8 + - - +
66A ARG* 3.0 38.8 + - - +
67A MET 3.2 0.2 - - - -
68A THR* 1.3 78.0 - - + +
70A LEU* 1.3 64.7 + - + +
72A ASP* 3.3 21.7 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 2.8 60.1 + - + +
69A GLU* 1.3 72.5 - - + +
71A TYR* 1.3 60.6 + - - +
72A ASP 3.1 7.4 + - - +
73A TYR* 3.3 15.6 - - - +
427A VAL* 3.8 12.5 - - + +
428A LYS 3.3 25.6 - - - +
429A GLY* 4.0 4.7 - - - +
430A ILE* 3.9 26.5 - - + -
486A VAL* 3.6 15.2 - - + +
490A ILE* 3.7 26.7 - - + -
493A ARG* 6.4 0.4 - - + -
494A HIS* 4.6 4.5 - - + +
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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