Contacts of the helix formed by residues 62 - 72 (chain A) in PDB entry 6WNX
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 ASP 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A MET* 2.7 24.8 + - + +
59A VAL 3.5 5.1 - - - +
61A THR* 1.3 74.2 + - - +
63A PRO* 1.4 72.0 - - - +
64A LEU* 3.1 23.9 + - - +
65A TRP* 3.0 37.1 + - + -
66A LYS 3.1 9.5 + - - -
389A GLU* 4.5 2.6 - - - +
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Residues in contact with PRO 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 VAL 5.1 0.2 - - - +
61A THR 3.4 10.0 - - - +
62A ASP* 1.4 85.6 - - - +
64A LEU* 1.3 55.5 + - - +
66A LYS* 3.3 15.0 - - + +
67A GLY* 2.7 31.4 + - - -
340A ASN* 6.0 1.3 - - - +
389A GLU* 4.0 21.4 - - - +
390A PHE* 5.2 1.0 - - - -
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Residues in contact with LEU 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 ASP* 3.1 21.6 + - - +
63A PRO* 1.3 79.2 - - - +
65A TRP* 1.3 57.3 + - - +
67A GLY* 3.2 1.7 + - - -
68A LEU* 2.9 35.9 + - + +
103A ILE* 4.0 38.8 - - + -
106A ILE* 4.9 7.4 - - + -
107A GLU* 4.5 0.9 - - - +
341A LYS* 3.7 24.0 - - - +
389A GLU* 3.7 26.1 - - + +
390A PHE* 3.6 29.2 - - + -
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Residues in contact with TRP 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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55A ILE* 4.4 10.3 - - + -
58A MET* 3.4 42.8 - - + +
59A VAL* 3.9 5.2 - - + -
62A ASP* 3.0 36.4 + - + +
64A LEU* 1.3 75.2 - - + +
66A LYS* 1.3 60.2 + - - +
68A LEU* 3.5 5.7 + - - +
69A SER* 2.9 31.7 + - - -
74A TRP* 3.5 11.7 - + - -
96A TYR* 3.5 43.3 - + - -
99A ILE* 3.6 44.4 - - + -
100A ILE* 3.6 23.6 - - + -
103A ILE* 3.4 21.7 - - + +
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Residues in contact with LYS 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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59A VAL* 3.8 29.4 - - + +
62A ASP 3.1 4.9 + - - -
63A PRO* 3.3 20.6 - - + +
65A TRP* 1.3 73.6 - - - +
67A GLY* 1.3 65.1 + - - +
69A SER* 2.6 26.9 + - - +
70A GLU* 3.3 30.3 + - - +
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Residues in contact with GLY 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 PRO 2.7 18.3 + - - -
64A LEU 3.2 3.8 + - - -
66A LYS* 1.3 71.2 - - - +
68A LEU* 1.3 55.9 + - - +
70A GLU* 2.9 32.1 + - - +
71A ARG* 3.0 20.2 + - - +
390A PHE* 3.9 16.8 - - - -
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Residues in contact with LEU 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 LEU* 2.9 21.0 + - + +
65A TRP* 3.8 2.0 - - - +
67A GLY* 1.3 70.7 - - - -
69A SER* 1.3 57.1 + - - +
71A ARG* 4.5 3.1 - - + +
72A ARG* 2.9 51.2 + - + +
74A TRP* 3.8 14.4 - - + -
99A ILE* 4.3 11.2 - - + -
102A ASP* 3.8 33.4 - - - +
103A ILE* 3.6 34.8 - - + -
106A ILE* 4.0 16.2 - - + -
390A PHE* 3.8 15.0 - - + -
407A LEU* 4.1 6.7 - - + -
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Residues in contact with SER 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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59A VAL* 4.1 12.5 - - - +
65A TRP 2.9 11.7 + - - -
66A LYS* 2.6 22.8 + - - +
68A LEU* 1.3 73.7 - - - +
70A GLU* 1.3 59.8 + - - +
73A GLY 3.0 15.8 + - - -
74A TRP* 3.0 36.4 + - - -
75A ASP* 2.9 40.6 + - - +
78A LEU* 4.7 0.9 - - - -
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Residues in contact with GLU 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 LYS* 3.4 41.4 + - - +
67A GLY* 2.9 14.0 + - - +
69A SER* 1.3 81.0 + - - +
71A ARG* 1.3 68.2 + - + +
73A GLY* 3.0 13.9 + - - -
75A ASP* 3.5 20.7 - - - +
76A GLN* 5.2 0.3 + - - -
137A ASP* 4.5 13.1 - - - +
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Residues in contact with ARG 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 GLY* 3.0 19.6 + - - +
68A LEU* 4.3 5.2 - - - +
70A GLU* 1.3 79.0 - - + +
72A ARG* 1.3 64.8 + - - +
137A ASP* 5.1 10.5 + - - -
154A LYS* 5.7 2.6 - - - +
388A ASP* 4.1 2.8 + - - -
390A PHE* 3.4 38.1 - - + +
391A GLN* 3.2 31.9 + - - +
405A ASP* 4.5 5.9 + - - -
407A LEU* 3.5 33.1 - - + +
408A ASN* 4.3 10.6 - - - +
164D THR 5.1 2.3 - - - +
198D GLU* 4.9 8.7 + - - -
199D VAL* 5.6 6.4 - - - +
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Residues in contact with ARG 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 LEU* 2.9 32.7 + - + +
71A ARG* 1.3 83.8 + - - +
73A GLY* 1.3 61.2 + - - +
74A TRP* 3.4 24.2 + - + +
102A ASP* 3.0 41.5 + - - +
407A LEU* 3.5 25.9 + - - +
408A ASN* 4.2 17.2 + - - -
161D LYS* 6.0 1.6 - - - +
164D THR* 2.9 43.2 + - - +
165D GLY* 3.8 1.1 + - - -
197D GLY 5.6 3.8 + - - -
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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