Contacts of the helix formed by residues 63 - 78 (chain D) in PDB entry 2WTK
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 GLN 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D GLU 3.9 5.7 + - - -
53D ILE* 3.0 45.1 + - + +
56D GLY* 4.7 2.2 - - - -
60D LYS* 4.0 27.7 + - - +
61D GLU 3.2 7.1 + - - +
62D PRO* 1.3 71.7 - - - +
64D THR* 1.3 67.0 + - - +
65D GLU* 2.9 5.1 + - + +
66D ALA* 3.0 35.9 + - + +
67D VAL* 3.1 11.7 + - - +
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PRO 3.2 8.5 + - - +
63D GLN* 1.3 70.9 - - - +
65D GLU* 1.3 77.1 + - + +
67D VAL* 3.9 7.0 + - - +
68D ALA* 3.5 18.2 + - - +
108D ARG* 5.2 2.1 + - - -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLN* 2.9 3.4 + - + +
64D THR* 1.3 90.0 + - + +
66D ALA* 1.3 65.8 + - - +
67D VAL 3.2 1.3 - - - -
68D ALA* 3.4 11.3 + - - +
69D GLN* 3.2 32.4 + - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 3.7 15.5 - - + +
53D ILE* 4.1 10.5 - - + +
63D GLN* 3.0 36.9 + - + +
65D GLU* 1.3 79.2 - - - +
67D VAL* 1.3 55.0 + - - +
69D GLN* 3.4 12.3 + - - +
70D LEU* 2.9 29.1 + - - +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ILE* 3.9 26.7 - - + +
54D LEU* 3.9 28.0 - - + +
62D PRO* 4.7 8.1 - - + -
63D GLN 3.1 21.0 + - - +
64D THR* 3.9 6.5 - - - +
66D ALA* 1.3 74.2 - - - +
68D ALA* 1.3 67.0 + - - +
70D LEU* 3.2 3.3 + - - +
71D ALA* 3.0 25.1 + - + +
104D ASN* 5.1 3.1 - - - +
105D ILE* 6.0 0.9 - - + -
108D ARG* 3.8 21.5 - - + +
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D THR 3.5 11.7 + - - +
65D GLU* 3.4 17.0 + - - +
67D VAL* 1.3 81.4 - - - +
69D GLN* 1.3 62.7 + - + +
71D ALA* 3.3 3.3 + - - +
72D GLN* 3.1 20.9 + - - +
108D ARG* 3.6 28.1 + - - +
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 5.2 4.6 - - - -
12D PRO* 4.0 28.6 - - + +
13D ALA 5.7 0.4 - - - +
65D GLU* 3.2 22.5 + - - +
66D ALA* 3.5 11.6 - - - +
68D ALA* 1.3 80.2 - - + +
70D LEU* 1.3 57.9 + - - +
72D GLN* 3.1 7.3 + - - +
73D GLU* 3.0 33.0 + - + +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 3.9 23.3 - - + +
15D ILE* 5.4 0.7 - - + -
16D VAL* 3.6 25.8 - - + -
50D MET* 4.0 31.0 - - + -
53D ILE* 4.0 22.2 - - + -
54D LEU* 3.9 32.1 - - + -
66D ALA 2.9 21.0 + - - +
67D VAL* 3.2 4.7 + - - +
69D GLN* 1.3 73.6 - - - +
71D ALA* 1.3 57.3 + - - +
73D GLU* 3.4 2.4 + - - +
74D LEU* 2.9 42.8 + - + +
105D ILE* 5.8 0.2 - - + -
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D VAL* 3.0 17.8 + - + +
68D ALA 3.5 4.0 - - - +
70D LEU* 1.3 74.2 - - - +
72D GLN* 1.3 65.0 + - - +
74D LEU* 3.1 12.0 + - - +
75D TYR* 3.0 41.7 + - + +
105D ILE* 4.7 11.6 - - + +
108D ARG* 3.7 30.7 - - - +
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Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ALA 3.1 9.3 + - - +
69D GLN* 3.1 10.5 + - - +
71D ALA* 1.3 78.8 - - - +
73D GLU* 1.3 63.7 + - + +
75D TYR* 3.5 21.0 + - - +
76D ASN* 3.1 63.6 + - - +
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO 4.5 0.9 - - - -
13D ALA* 3.5 47.3 - - + +
16D VAL* 3.8 23.4 - - + +
17D LYS* 6.0 0.2 - - - +
69D GLN* 3.0 20.3 + - + +
70D LEU* 3.7 5.4 - - - +
72D GLN* 1.3 74.4 - - + +
74D LEU* 1.3 54.8 + - - +
76D ASN* 3.3 9.4 + - - +
77D SER* 2.5 41.0 + - - -
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D VAL* 4.0 18.6 - - + -
50D MET* 4.1 15.9 - - + -
70D LEU* 2.9 34.2 + - + +
71D ALA* 3.1 5.6 + - - +
73D GLU* 1.3 76.9 - - - +
75D TYR* 1.3 65.4 + - + +
77D SER* 2.8 16.0 + - - -
78D GLY* 3.4 6.1 + - - -
79D LEU* 3.9 23.3 + - + -
80D LEU* 4.2 26.8 + - + +
83D LEU* 5.2 3.8 - - + -
101D ILE* 4.4 12.3 - - + -
105D ILE* 3.7 39.7 - - + -
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Residues in contact with TYR 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ALA* 3.0 29.0 + - + +
72D GLN* 3.7 26.0 - - - +
74D LEU* 1.3 80.2 - - + +
76D ASN* 1.3 68.9 + - - +
77D SER 3.3 0.3 + - - -
78D GLY* 3.4 6.9 + - - -
80D LEU* 4.3 13.5 - - + -
105D ILE* 5.2 3.8 - - + +
108D ARG* 3.9 15.0 - - - -
115D PRO* 3.3 31.6 - - + +
116D THR* 2.9 36.5 + - - -
119D TYR* 3.7 47.0 + + + -
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Residues in contact with ASN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LYS* 5.7 0.5 + - - -
72D GLN* 3.1 44.5 + - - +
73D GLU* 4.0 10.6 + - - +
75D TYR* 1.3 78.3 - - - +
77D SER* 1.3 60.9 + - - +
78D GLY 3.4 0.3 + - - -
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Residues in contact with SER 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D VAL* 3.4 20.8 - - - +
20D LYS* 3.5 37.7 - - - +
73D GLU* 2.5 26.4 + - - -
74D LEU* 2.8 17.2 + - - -
75D TYR 3.3 0.2 - - - -
76D ASN* 1.3 74.2 - - - +
78D GLY* 1.3 55.8 + - - +
79D LEU* 2.9 21.8 + - - +
82D THR* 5.3 0.5 + - - -
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Residues in contact with GLY 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LEU 3.4 1.4 + - - -
75D TYR 3.4 6.9 + - - -
76D ASN 3.3 4.6 + - - -
77D SER* 1.3 75.8 - - - +
79D LEU* 1.3 56.1 + - - +
80D LEU 3.1 3.6 - - - -
81D SER* 2.8 27.0 + - - -
82D THR* 3.2 14.1 + - - -
119D TYR* 3.8 17.0 - - - -
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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