Contacts of the helix formed by residues 63 - 74 (chain D) in PDB entry 4NY0
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 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D ALA 3.4 5.1 + - - +
62D THR* 1.3 78.3 - - - +
64D VAL* 1.3 59.6 + - - +
65D ARG* 3.5 16.0 + - - +
66D GLY* 2.8 47.9 + - - -
67D ILE 3.2 8.5 + - - -
100D VAL 3.5 15.5 - - - +
101D ASP* 3.9 12.7 - - - +
102D MET 3.3 14.6 - - - +
103D GLY* 4.0 2.0 - - - -
104D VAL* 3.6 4.4 - - - +
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Residues in contact with VAL 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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63D ASP* 1.3 71.6 - - - +
65D ARG* 1.3 62.1 + - - +
67D ILE* 3.1 4.3 + - - +
68D ILE* 2.9 31.5 + - + +
85D LEU* 3.6 38.4 - - + +
98D LEU* 3.9 29.2 - - + +
99D HIS 3.3 23.6 - - - +
100D VAL* 3.4 5.1 + - + -
102D MET* 2.9 22.6 + - + +
104D VAL* 4.1 15.5 - - + +
107D VAL* 5.1 2.5 - - + -
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Residues in contact with ARG 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 ASP* 3.1 15.8 + - - +
64D VAL* 1.3 75.9 - - - +
66D GLY* 1.3 58.2 + - - +
68D ILE* 3.4 6.8 + - - +
69D GLN* 3.0 51.1 + - + +
100D VAL* 3.1 48.2 + - + +
101D ASP* 3.0 24.8 + - - -
349D ARG* 3.9 7.5 - - - +
355D SER* 3.2 46.0 + - - +
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Residues in contact with GLY 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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62D THR* 4.3 7.4 - - - -
63D ASP* 2.8 22.6 + - - -
65D ARG* 1.3 73.8 - - - +
67D ILE* 1.3 64.3 + - - -
69D GLN* 3.4 12.0 + - - +
70D LYS* 3.1 37.4 + - - +
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Residues in contact with ILE 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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37D LEU* 4.1 14.6 - - + -
39D VAL* 4.0 16.6 - - + -
56D ILE* 3.5 25.3 - - + +
58D HIS* 3.9 22.9 - - + -
62D THR* 4.0 4.0 - - + +
63D ASP 3.2 2.2 + - - -
64D VAL* 3.1 9.3 + - - +
66D GLY* 1.3 73.9 - - - +
68D ILE* 1.3 64.3 + - - +
70D LYS* 3.2 5.9 + - + +
71D ILE* 3.1 41.7 + - + +
85D LEU* 4.2 16.2 - - + -
104D VAL* 3.4 29.8 - - + -
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Residues in contact with ILE 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 VAL* 2.9 31.1 + - + +
65D ARG* 3.7 7.9 - - - +
67D ILE* 1.3 77.2 - - + +
69D GLN* 1.3 58.1 + - - +
71D ILE* 3.4 3.7 + - - +
72D VAL* 3.0 32.7 + - + +
80D VAL* 4.3 17.3 - - + +
83D TYR* 3.4 42.4 - - + +
84D GLY* 3.9 17.3 - - - -
85D LEU* 4.7 3.8 - - + -
100D VAL* 4.3 13.2 - - + -
124D LEU* 3.8 20.4 - - + -
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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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353B GLY* 4.4 21.0 + - - +
65D ARG* 3.0 43.4 + - + +
66D GLY* 3.8 10.5 - - - +
67D ILE 3.3 0.2 - - - -
68D ILE* 1.3 76.7 - - - +
70D LYS* 1.3 58.6 + - + +
72D VAL* 3.9 7.0 - - - -
73D ASP* 2.8 51.2 + - - +
80D VAL* 4.8 6.9 - - + +
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Residues in contact with LYS 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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56D ILE* 3.7 32.6 - - + +
57D ARG 3.2 19.5 + - - +
58D HIS* 4.4 1.8 - - - +
62D THR* 4.1 19.1 + - - +
66D GLY* 3.1 23.2 + - - +
67D ILE* 3.2 6.5 + - + +
69D GLN* 1.3 77.2 - - + +
71D ILE* 1.3 61.8 + - - +
73D ASP* 4.2 5.6 + - - +
74D SER* 4.5 8.0 + - - -
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Residues in contact with ILE 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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39D VAL* 3.6 39.0 - - + +
41D HIS* 4.0 23.8 - - + -
43D PHE* 4.4 5.6 - - + -
54D SER* 4.2 7.5 + - - +
56D ILE* 3.4 21.3 - - + -
67D ILE* 3.1 26.6 + - + +
68D ILE 3.7 4.7 - - - +
70D LYS* 1.3 79.8 - - - +
72D VAL* 1.3 61.7 + - - +
73D ASP 3.8 0.2 + - - -
74D SER* 4.0 5.2 - - - -
75D HIS* 3.5 19.2 + - + -
85D LEU* 5.5 0.2 - - + -
124D LEU* 3.9 28.9 - - + -
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Residues in contact with VAL 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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43D PHE* 4.1 16.2 - - + -
68D ILE* 3.0 29.8 + - + +
69D GLN* 3.6 10.1 - - + +
71D ILE* 1.3 75.5 - - - +
73D ASP* 1.3 71.6 + - - +
74D SER 3.1 2.7 - - - -
75D HIS* 2.9 18.4 + - - +
76D LYS 3.6 3.8 + - - -
77D VAL* 3.8 21.2 + - + +
80D VAL* 4.0 29.8 - - + -
83D TYR* 4.4 11.2 - - + -
124D LEU* 3.9 24.9 - - + -
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Residues in contact with ASP 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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353B GLY 5.2 1.6 - - - +
354B THR* 5.0 6.4 - - - +
355B SER* 3.0 36.2 + - - +
69D GLN* 2.8 36.8 + - - +
70D LYS* 4.2 4.2 + - - +
71D ILE 3.5 0.4 - - - -
72D VAL* 1.3 78.3 - - - +
74D SER* 1.3 62.7 + - - +
75D HIS 3.1 1.0 + - - -
76D LYS* 3.2 15.2 + - - +
77D VAL 5.3 2.0 - - - +
80D VAL* 5.2 0.9 - - - +
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Residues in contact with SER 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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70D LYS 4.5 7.1 + - - -
71D ILE 4.0 8.0 + - - -
73D ASP* 1.3 79.1 - - - +
75D HIS* 1.3 77.4 + - - +
76D LYS* 3.5 4.4 + - - +
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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