Contacts of the helix formed by residues 64 - 74 (chain A) in PDB entry 3N9Y
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PRO* 4.7 1.8 + - + -
62A VAL* 4.8 0.2 - - - +
63A ILE* 1.3 80.5 - - + +
65A PRO* 1.4 73.3 - - - +
66A GLU* 2.9 32.2 + - - +
67A ASP* 2.9 25.0 + - - +
68A VAL* 3.0 11.5 + - - +
366A ARG* 3.0 34.5 + - - +
389A PHE* 3.6 24.0 - - + -
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Residues in contact with PRO 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 ILE 3.4 8.7 - - - +
64A ASP* 1.4 88.3 - - - +
66A GLU* 1.3 57.0 + - + +
68A VAL* 3.2 13.5 + - + +
69A ALA* 2.9 29.3 + - - +
383A LEU* 4.0 10.3 - - + -
389A PHE* 3.6 19.1 - - + -
410A TYR* 3.6 13.5 - - + +
411A PHE* 3.8 13.5 - - + +
412A ARG* 3.5 46.9 - - - +
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Residues in contact with GLU 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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64A ASP* 2.9 22.1 + - - +
65A PRO* 1.3 77.0 - - + +
67A ASP* 1.3 65.6 + - - +
69A ALA* 3.5 7.2 + - - +
70A LEU* 3.3 27.2 + - + +
407A ASN* 5.4 4.3 - - - +
410A TYR* 3.7 23.6 - - + -
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Residues in contact with ASP 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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48A PRO 4.7 3.8 - - - +
62A VAL* 4.3 23.1 - - + +
64A ASP* 2.9 14.9 + - - +
66A GLU* 1.3 77.8 - - - +
68A VAL* 1.3 66.1 + - - +
70A LEU* 3.2 9.4 + - - +
71A LEU* 3.0 22.4 + - - +
365A LEU* 3.9 21.0 - - + +
366A ARG* 3.0 58.0 + - - +
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Residues in contact with VAL 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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62A VAL* 4.6 5.2 - - + -
63A ILE 4.5 3.8 - - - +
64A ASP 3.0 16.9 + - - +
65A PRO* 3.2 16.1 + - + +
67A ASP* 1.3 76.8 - - - +
69A ALA* 1.3 62.8 + - - +
71A LEU* 3.1 9.0 + - - +
72A PHE* 3.0 48.4 + - + -
378A VAL* 3.5 34.3 - - + -
383A LEU* 5.1 0.7 - - + -
411A PHE* 4.0 12.6 - - + -
414A LEU* 4.1 18.2 - - + -
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Residues in contact with ALA 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 PRO 2.9 16.5 + - - +
66A GLU* 3.6 7.0 - - - +
67A ASP 3.2 0.2 - - - -
68A VAL* 1.3 76.9 - - - +
70A LEU* 1.3 59.4 + - + +
72A PHE* 3.4 2.1 + - - +
73A LYS* 2.8 31.7 + - - +
410A TYR* 3.6 28.3 - - + +
411A PHE* 3.7 27.6 - - + -
82C TYR* 5.6 3.4 - - + +
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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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66A GLU 3.3 14.8 + - - +
67A ASP* 3.2 13.6 + - - +
69A ALA* 1.3 77.2 - - + +
71A LEU* 1.3 65.9 + - - +
73A LYS* 3.3 22.0 + - + +
74A SER* 3.3 23.6 + - - -
363A LEU* 4.3 11.5 - - + +
364A VAL 4.5 6.3 - - - +
365A LEU* 3.8 24.7 - - + -
366A ARG 6.0 0.4 - - - +
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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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62A VAL* 5.1 1.6 - - + -
67A ASP 3.0 13.5 + - - +
68A VAL* 3.1 8.7 + - - +
70A LEU* 1.3 75.7 - - - +
72A PHE* 1.3 72.5 + - + +
74A SER* 3.0 20.1 + - - -
75A GLU* 3.6 7.1 + - - +
356A GLN* 5.8 0.9 - - - -
357A ARG* 4.3 22.3 - - + +
359A LEU* 3.5 31.2 - - + -
363A LEU* 4.2 10.8 - - + +
365A LEU* 5.1 2.5 - - + -
376A VAL* 3.8 35.0 - - + +
378A VAL* 3.7 28.9 - - + -
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Residues in contact with PHE 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 VAL* 3.0 45.4 + - + +
69A ALA 4.2 2.2 - - - +
71A LEU* 1.3 82.6 - - + +
73A LYS* 1.3 64.9 + - - +
74A SER 3.3 0.2 - - - -
75A GLU* 3.3 37.3 - - - +
355A LEU* 3.9 33.9 - - + -
356A GLN 6.2 0.2 - - - -
357A ARG* 3.9 28.9 - - + -
378A VAL* 4.6 4.9 - - + -
411A PHE* 4.1 13.5 - + + -
414A LEU* 4.7 2.7 - - + -
418A TRP* 3.3 62.8 - + + -
82C TYR* 5.4 0.3 - - - -
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Residues in contact with LYS 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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69A ALA 2.8 18.8 + - - +
70A LEU* 3.6 24.1 - - + +
71A LEU 3.3 0.2 - - - -
72A PHE* 1.3 78.1 - - - +
74A SER* 1.3 57.8 + - - +
75A GLU 3.3 3.9 + - - +
411A PHE* 5.9 0.2 - - - -
82C TYR* 4.1 59.6 + - + +
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Residues in contact with SER 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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70A LEU 3.3 9.3 + - - -
71A LEU 3.0 13.2 + - - -
72A PHE 3.3 0.2 - - - -
73A LYS* 1.3 76.5 - - - +
75A GLU* 1.3 65.6 + - - +
76A GLY* 3.5 1.9 + - - -
359A LEU* 4.7 6.9 - - - +
360A VAL* 5.2 6.2 + - - +
361A ASN* 5.0 15.7 + - - +
362A ASP 6.0 0.7 - - - -
363A LEU* 4.1 25.6 - - - +
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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