Contacts of the helix formed by residues 60 - 71 (chain A) in PDB entry 1EQQ
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 PHE 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A MET* 5.3 4.9 - - - -
28A ALA 3.3 4.5 - - - -
29A VAL* 3.5 35.4 - - + -
58A VAL* 3.5 10.3 - - + -
59A LEU* 1.3 79.1 - - - +
61A GLY* 1.3 72.9 + - - +
62A LYS 3.4 0.3 + - - -
63A LEU* 3.4 12.0 + - - +
64A ALA* 3.1 9.0 + - - -
84A ARG* 3.1 26.9 - - - -
101A VAL* 3.2 33.0 - - + -
102A VAL 4.2 9.1 + - - +
103A VAL* 4.3 21.3 - - + -
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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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28A ALA* 3.2 24.1 + - - +
60A PHE* 1.3 78.8 - - - +
62A LYS* 1.3 66.2 + - - +
64A ALA* 2.9 16.1 + - - +
65A GLU* 3.2 4.7 + - - +
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Residues in contact with LYS 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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60A PHE 3.4 0.4 + - - -
61A GLY* 1.3 68.3 - - - -
63A LEU* 1.3 78.8 + - + +
65A GLU* 2.5 43.3 + - - +
66A VAL* 2.6 26.6 + - + +
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Residues in contact with LEU 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 LEU* 4.0 21.5 - - + +
60A PHE 3.4 10.5 + - - +
62A LYS* 1.3 98.0 - - + +
64A ALA* 1.3 64.4 + - - +
66A VAL* 3.7 13.2 - - + -
67A ALA* 2.7 27.6 + - - +
102A VAL* 5.3 9.0 - - + +
104A ASN* 5.9 4.9 - - - +
106A GLY 5.9 1.1 - - - +
107A GLY* 5.0 8.1 - - - -
108A THR* 3.2 39.5 - - + +
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Residues in contact with ALA 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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20A VAL* 5.2 2.6 - - + +
28A ALA* 3.2 34.5 - - + +
29A VAL 4.0 0.2 - - - -
30A ALA* 3.5 19.4 - - - +
59A LEU* 3.7 12.9 - - - +
60A PHE* 3.1 9.6 + - - -
61A GLY 2.9 16.2 + - - +
63A LEU* 1.3 80.6 - - - +
65A GLU* 1.3 59.7 - - - +
67A ALA* 3.2 4.0 - - - +
68A SER* 3.0 19.3 + - - -
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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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20A VAL* 6.1 1.1 - - - -
22A TYR* 4.3 16.5 + - - +
28A ALA* 3.9 16.1 - - + +
61A GLY 3.6 9.9 - - - +
62A LYS* 2.5 25.4 + - + +
64A ALA* 1.3 69.4 - - - +
66A VAL* 1.3 68.8 + - + +
68A SER* 2.8 20.6 + - - -
69A GLU* 2.8 29.0 + - + +
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Residues in contact with VAL 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 LYS* 2.6 48.5 + - + +
63A LEU* 3.4 15.3 - - + +
65A GLU* 1.3 72.1 - - + +
67A ALA* 1.3 67.2 + - - +
69A GLU* 3.0 6.3 + - - +
70A TYR* 2.9 38.0 + - + +
71A LEU* 4.7 2.7 - - + -
108A THR* 5.4 8.7 - - + -
110A GLN* 5.6 5.8 - - - +
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Residues in contact with ALA 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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18A PRO* 3.3 11.1 - - + +
30A ALA* 3.8 6.5 - - + -
32A ILE* 4.6 0.7 - - + -
59A LEU* 3.2 35.7 - - + -
63A LEU 2.7 9.4 + - - +
64A ALA 3.2 8.5 - - - +
66A VAL* 1.3 73.0 - - - +
68A SER* 1.3 58.5 + - - +
71A LEU* 2.6 56.8 + - + +
108A THR* 6.0 0.2 - - + -
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Residues in contact with SER 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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18A PRO* 4.1 6.1 - - - +
20A VAL* 3.2 39.7 - - - +
22A TYR* 6.1 0.2 - - - -
64A ALA 3.0 6.5 + - - -
65A GLU* 2.8 19.2 + - - -
67A ALA* 1.3 76.3 - - - +
69A GLU* 1.3 63.4 + - - +
71A LEU 4.6 0.9 - - - +
72A ARG* 3.4 13.7 + - - -
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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* 2.8 31.4 + - - +
66A VAL* 4.7 1.6 - - - -
68A SER* 1.3 72.3 - - - +
70A TYR* 1.3 101.0 + - + +
72A ARG* 2.6 22.8 + - - +
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Residues in contact with TYR 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 VAL* 2.9 25.7 + - + +
69A GLU* 1.3 125.4 + - + +
71A LEU* 1.3 71.4 + - + +
72A ARG* 3.6 13.0 + - - +
75A SER* 4.9 1.9 + - - -
110A GLN* 4.6 18.3 + - - +
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Residues in contact with LEU 71 (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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14A LEU* 3.8 13.9 - - + -
18A PRO* 2.9 29.1 - - + +
32A ILE* 4.9 5.2 - - + -
59A LEU* 4.7 5.8 - - + -
66A VAL* 4.5 3.8 - - + +
67A ALA* 2.6 51.4 + - + +
68A SER 4.6 0.2 - - - +
70A TYR* 1.3 78.4 - - + +
72A ARG* 1.3 73.2 + - - +
75A SER* 4.7 5.8 - - - -
77A VAL* 4.1 20.9 - - + -
108A THR* 4.4 19.1 - - + +
110A GLN* 3.1 32.5 - - + +
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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