Contacts of the helix formed by residues 64 - 74 (chain B) in PDB entry 3NA1
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO* 4.7 2.0 + - + -
62B VAL* 4.6 0.2 - - - +
63B ILE* 1.3 80.1 - - + +
65B PRO* 1.3 72.6 - - - +
66B GLU* 2.7 37.5 + - - +
67B ASP* 2.9 27.6 + - - +
68B VAL* 3.0 12.9 + - - +
366B ARG* 2.6 33.5 + - - +
389B PHE* 3.6 27.1 - - + -
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Residues in contact with PRO 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE 3.4 8.7 - - - +
64B ASP* 1.3 88.5 - - - +
66B GLU* 1.3 55.9 + - - +
68B VAL* 3.3 12.9 + - + +
69B ALA* 2.9 29.5 + - - +
383B LEU* 3.8 10.8 - - + -
389B PHE* 3.6 19.1 - - + -
410B TYR* 3.5 27.1 - - + +
411B PHE* 3.8 12.2 - - + +
412B ARG* 3.1 36.3 - - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASP* 2.7 24.2 + - - +
65B PRO* 1.3 73.2 - - - +
67B ASP* 1.3 62.8 + - - +
69B ALA* 3.5 7.4 - - - +
70B LEU* 3.4 28.6 + - + +
366B ARG* 5.5 1.1 - - - +
410B TYR* 3.9 29.1 + - - -
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO 4.8 2.8 - - - +
62B VAL* 3.9 25.7 - - + +
64B ASP* 2.9 21.1 + - - +
66B GLU* 1.3 76.7 - - - +
68B VAL* 1.3 64.5 + - - +
70B LEU* 3.3 7.9 + - - +
71B LEU* 2.9 22.9 + - - +
365B LEU* 3.8 26.0 - - + +
366B ARG* 2.9 47.2 + - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.1 9.0 - - + -
63B ILE 4.6 3.4 - - - +
64B ASP 3.0 17.3 + - - +
65B PRO* 3.3 15.2 + - + +
67B ASP* 1.3 76.5 - - - +
69B ALA* 1.3 63.7 + - - +
71B LEU* 3.1 8.2 + - - +
72B PHE* 3.0 50.2 + - + -
378B VAL* 3.6 28.9 - - + -
383B LEU* 4.9 0.7 - - + -
411B PHE* 4.0 13.7 - - + -
414B LEU* 4.1 19.5 - - + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PRO 2.9 13.1 + - - +
66B GLU* 3.5 13.0 - - - +
68B VAL* 1.3 75.7 - - - +
70B LEU* 1.3 58.3 + - + +
72B PHE* 3.4 1.4 + - - +
73B LYS* 2.9 43.3 + - + +
410B TYR* 3.5 29.2 - - + +
411B PHE* 3.7 24.6 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU* 3.4 18.3 + - + +
67B ASP* 3.3 13.3 + - - +
69B ALA* 1.3 75.6 - - + +
71B LEU* 1.3 65.3 + - - +
73B LYS* 3.5 19.7 + - + +
74B SER* 3.3 24.4 + - - -
363B LEU* 4.2 14.6 - - + +
364B VAL 4.4 8.1 - - - +
365B LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 5.6 1.6 - - + -
67B ASP 2.9 13.7 + - - +
68B VAL* 3.1 9.6 + - - +
70B LEU* 1.3 77.6 - - - +
72B PHE* 1.3 70.4 + - + +
74B SER* 3.2 16.5 + - - -
75B GLU* 3.8 7.3 + - - +
356B GLN* 5.7 0.4 - - - -
357B ARG* 4.4 26.6 - - + +
359B LEU* 3.6 29.4 - - + -
363B LEU* 4.2 11.4 - - + +
365B LEU* 5.2 2.0 - - + -
376B VAL* 3.9 34.5 - - + +
378B VAL* 3.8 28.7 - - + -
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 3.0 47.3 + - + +
71B LEU* 1.3 80.3 - - + +
73B LYS* 1.3 65.0 + - - +
74B SER 3.3 0.2 - - - -
75B GLU* 3.2 36.0 - - - +
355B LEU* 3.8 34.3 - - + -
357B ARG* 4.0 27.1 - - + -
378B VAL* 4.4 7.9 - - + -
411B PHE* 4.2 9.9 - + + -
414B LEU* 4.8 1.3 - - + -
418B TRP* 3.2 75.1 - + + -
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA* 2.9 29.8 + - + +
70B LEU* 3.6 24.2 - - + +
71B LEU 3.3 0.2 - - - -
72B PHE* 1.3 78.4 - - - +
74B SER* 1.3 56.2 + - - +
75B GLU 3.2 6.5 + - - +
410B TYR* 4.6 12.7 + - - -
411B PHE* 5.0 3.6 - - + -
418B TRP* 5.2 3.4 - - + -
81D ALA 3.3 33.9 - - - +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU 3.3 10.6 + - - -
71B LEU 3.2 12.3 + - - -
72B PHE 3.3 0.6 - - - -
73B LYS* 1.3 77.2 - - - +
75B GLU* 1.3 60.6 + - - +
76B GLY 3.7 2.1 + - - -
359B LEU* 4.6 8.5 - - - +
360B VAL* 5.2 10.4 + - - +
361B ASN* 5.5 9.8 + - - +
362B ASP 6.1 0.7 - - - -
363B LEU* 4.0 25.0 - - - +
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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