Contacts of the helix formed by residues 63 - 78 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ILE 4.6 2.0 + - - -
61A GLU 3.6 11.9 - - - +
62A PRO* 1.3 71.0 - - - +
64A THR* 1.3 64.5 + - - +
65A GLU* 3.4 2.0 - - + +
66A ALA* 3.3 19.1 + - + +
67A VAL* 3.2 21.8 + - - +
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Residues in contact with THR 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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62A PRO 4.3 9.0 - - - +
63A GLN* 1.3 72.5 - - - +
65A GLU* 1.3 64.9 + - - +
67A VAL* 3.5 9.1 + - - +
68A ALA* 3.2 21.0 + - - +
108A ARG* 5.1 2.3 + - - -
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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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63A GLN* 3.4 1.6 - - + +
64A THR* 1.3 77.9 + - - +
66A ALA* 1.3 67.5 + - - +
68A ALA* 3.0 19.4 + - + +
69A GLN* 3.1 30.5 + - - +
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Residues in contact with ALA 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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12A PRO* 3.5 19.8 - - + +
53A ILE* 4.4 17.9 - - + -
63A GLN* 3.3 22.9 + - + +
65A GLU* 1.3 77.8 - - - +
67A VAL* 1.3 57.0 + - - +
69A GLN* 3.3 2.0 + - - -
70A LEU* 2.9 30.3 + - - +
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Residues in contact with VAL 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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53A ILE* 3.6 27.6 - - + +
54A LEU* 3.9 23.3 - - + +
62A PRO* 4.2 11.2 - - + -
63A GLN 3.2 15.6 + - - +
64A THR* 3.7 9.6 - - - +
65A GLU 3.2 0.8 - - - -
66A ALA* 1.3 76.6 - - - +
68A ALA* 1.3 56.4 + - - +
70A LEU* 3.3 6.2 + - - +
71A ALA* 2.9 30.4 + - + +
104A ASN* 5.1 2.9 - - - +
105A ILE* 5.8 0.9 - - + -
108A ARG* 4.0 21.5 - - + +
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Residues in contact with ALA 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 THR 3.2 12.4 + - - +
65A GLU* 3.0 18.2 + - + +
67A VAL* 1.3 77.1 - - - +
69A GLN* 1.3 59.1 + - - +
71A ALA* 3.7 2.4 - - - +
72A GLN* 3.1 25.8 + - - +
108A ARG* 3.3 30.2 + - - +
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Residues in contact with GLN 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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12A PRO* 4.0 17.0 - - + -
13A ALA* 5.8 2.5 - - + +
65A GLU* 3.1 31.6 + - - +
66A ALA* 3.9 3.8 - - - +
68A ALA* 1.3 77.0 - - - +
70A LEU* 1.3 66.3 + - - +
71A ALA 3.3 0.2 - - - -
72A GLN* 3.3 10.4 + - - +
73A GLU* 3.0 46.0 + - + +
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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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12A PRO* 3.6 22.3 - - + +
15A ILE* 5.5 0.4 - - + -
16A VAL* 3.8 24.0 - - + -
50A MET* 3.9 34.5 - - + +
53A ILE* 3.8 27.1 - - + -
54A LEU* 3.9 26.5 - - + -
66A ALA 2.9 17.4 + - - +
67A VAL* 3.7 4.5 - - - +
69A GLN* 1.3 76.8 - - - +
71A ALA* 1.3 58.1 + - - +
73A GLU* 3.3 2.0 + - - +
74A LEU* 2.8 43.0 + - + +
105A ILE* 5.6 0.7 - - + -
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Residues in contact with ALA 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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67A VAL* 2.9 18.1 + - + +
68A ALA 3.7 3.6 - - - +
70A LEU* 1.3 77.1 - - - +
72A GLN* 1.3 61.7 + - - +
74A LEU* 3.3 9.7 + - - +
75A TYR* 3.0 41.8 + - + +
105A ILE* 5.0 11.4 - - + +
108A ARG* 3.7 33.0 - - - +
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Residues in contact with GLN 72 (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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68A ALA 3.1 15.5 + - - +
69A GLN* 3.3 14.8 + - - +
70A LEU 3.3 0.4 - - - -
71A ALA* 1.3 78.0 - - - +
73A GLU* 1.3 59.1 + - - +
75A TYR* 3.1 25.0 + - - +
76A ASN* 2.8 65.6 + - - +
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Residues in contact with GLU 73 (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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12A PRO* 5.0 0.2 - - + -
13A ALA* 3.8 35.2 - - + +
16A VAL* 3.8 20.4 - - + +
69A GLN* 3.0 36.4 + - + +
70A LEU* 3.7 3.6 - - - +
72A GLN* 1.3 73.3 - - - +
74A LEU* 1.3 59.9 + - - +
76A ASN* 4.0 16.9 + - - +
77A SER* 2.7 41.6 + - - -
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Residues in contact with LEU 74 (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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16A VAL* 4.1 2.7 - - + -
50A MET* 3.9 26.5 - - + -
70A LEU* 2.8 33.1 + - + +
71A ALA* 3.5 5.4 - - - +
73A GLU* 1.3 76.0 - - - +
75A TYR* 1.3 66.7 + - + +
77A SER* 3.7 3.6 + - - -
78A GLY* 3.6 11.6 + - - -
79A LEU* 3.8 29.4 + - + -
80A LEU* 3.8 29.9 + - + +
83A LEU* 5.2 2.2 - - + -
101A ILE* 4.4 12.3 - - + -
105A ILE* 3.8 37.9 - - + -
119A TYR* 4.6 2.1 + - - -
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Residues in contact with TYR 75 (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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71A ALA* 3.0 32.0 + - + +
72A GLN* 3.1 27.3 + - - +
74A LEU* 1.3 80.5 - - + +
76A ASN* 1.3 69.8 + - - +
77A SER 3.0 1.6 + - - -
78A GLY 3.3 7.3 + - - -
80A LEU* 4.9 1.3 - - + -
105A ILE* 4.5 9.2 - - + -
108A ARG* 4.3 7.7 - - - -
115A PRO* 3.4 22.4 - - + +
116A THR* 2.7 53.1 + - + -
119A TYR* 3.7 51.3 + + + -
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Residues in contact with ASN 76 (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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72A GLN* 2.8 57.1 + - - +
73A GLU* 4.0 19.6 + - - +
75A TYR* 1.3 72.9 - - - +
77A SER* 1.3 60.2 + - - +
78A GLY 3.8 0.2 + - - -
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Residues in contact with SER 77 (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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16A VAL* 3.3 26.1 - - - +
20A LYS* 3.9 34.9 + - - +
73A GLU* 2.7 23.9 + - - -
74A LEU 3.7 0.2 + - - -
76A ASN* 1.3 78.3 - - - +
78A GLY* 1.3 61.8 + - - +
79A LEU* 3.2 14.0 + - - +
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Residues in contact with GLY 78 (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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74A LEU 3.6 2.6 + - - -
75A TYR 3.3 12.2 + - - -
76A ASN 3.5 0.6 - - - -
77A SER* 1.3 77.6 + - - +
79A LEU* 1.3 64.5 + - - +
80A LEU 3.3 2.7 - - - -
81A SER* 2.9 22.0 + - - -
82A THR* 3.1 14.1 + - - -
119A TYR* 4.2 10.3 - - - -
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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