Contacts of the helix formed by residues 66 - 80 (chain B) in PDB entry 5N4D
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 ALA 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ASP 4.9 1.8 + - - -
64B GLN 3.8 4.4 + - - -
65B ASN* 1.3 71.3 + - - +
67B ASP* 1.3 68.7 + - - +
68B ILE 3.2 0.9 + - - -
69B GLN* 3.5 15.8 + - - +
70B LYS* 3.9 19.3 + - - +
720B ARG* 4.5 4.2 - - - +
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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
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65B ASN* 3.0 15.0 + - - +
66B ALA* 1.3 81.3 - - - +
68B ILE* 1.3 63.4 + - - +
70B LYS* 3.2 9.9 + - - +
71B LEU* 2.9 25.5 + - + +
518B TYR* 4.3 10.0 + - - +
716B GLY* 6.2 0.9 - - - -
720B ARG* 4.6 9.6 + - - -
724B LEU 4.5 6.9 - - - +
725B GLU* 4.3 10.4 - - - +
726B LEU* 3.5 43.9 + - + +
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Residues in contact with ILE 68 (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 LEU* 3.6 54.1 - - + +
65B ASN* 3.3 28.2 + - + +
66B ALA 3.2 1.4 - - - -
67B ASP* 1.3 76.3 - - - +
69B GLN* 1.3 59.5 + - - +
71B LEU* 3.1 7.5 + - - +
72B ALA* 2.9 25.2 + - + +
709B LYS* 6.4 0.7 - - + -
712B ALA* 3.6 29.2 - - + +
713B ASP* 3.4 25.6 - - - +
716B GLY* 3.9 6.7 - - - -
717B PHE 4.7 0.7 - - - +
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Residues in contact with GLN 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 ASN 4.7 0.4 + - - -
66B ALA* 3.5 10.8 + - - +
67B ASP 3.2 1.0 - - - -
68B ILE* 1.3 79.7 - - - +
70B LYS* 1.3 62.4 + - + +
72B ALA* 3.3 13.5 + - - +
73B GLU* 3.1 41.1 + - - +
76B ARG* 5.9 1.6 + - - -
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Residues in contact with LYS 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 ALA* 4.1 18.4 - - - +
67B ASP* 3.2 13.4 + - - +
69B GLN* 1.3 75.0 - - + +
71B LEU* 1.3 66.7 - - - +
73B GLU* 3.3 23.7 + - - +
74B LYS* 3.1 32.7 + - - +
726B LEU* 3.5 30.1 - - + -
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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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67B ASP* 2.9 18.3 + - + +
68B ILE* 3.1 6.9 + - - +
70B LYS* 1.3 74.2 - - - +
72B ALA* 1.3 60.4 + - - +
74B LYS* 3.2 17.0 + - + -
75B PHE* 2.8 61.8 + - + -
514B PHE* 5.1 0.7 - - + -
517B THR* 4.4 6.7 - - + -
518B TYR* 3.8 37.2 - - + +
712B ALA* 4.1 7.4 - - + +
715B TRP* 4.0 5.8 - - + +
716B GLY* 3.5 36.8 - - - +
726B LEU* 4.6 3.8 - - + -
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Residues in contact with ALA 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 ILE* 2.9 10.6 + - + +
69B GLN* 3.6 18.8 - - - +
70B LYS 3.3 0.2 - - - -
71B LEU* 1.3 76.8 - - - +
73B GLU* 1.3 57.1 + - + +
75B PHE* 4.5 0.7 - - - -
76B ARG* 2.9 48.2 + - - +
708B VAL* 3.8 13.7 - - + +
709B LYS* 5.2 6.1 - - + -
712B ALA* 3.5 21.8 - - + +
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Residues in contact with GLU 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 GLN* 3.1 35.7 + - + +
70B LYS* 3.6 22.5 + - - +
71B LEU 3.2 0.2 - - - -
72B ALA* 1.3 77.6 - - + +
74B LYS* 1.3 62.5 + - + +
76B ARG* 3.8 18.9 + - - +
77B ALA* 3.2 22.7 + - - +
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Residues in contact with LYS 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 LYS* 3.1 22.6 + - - +
71B LEU* 3.2 14.8 + - + +
73B GLU* 1.3 75.8 - - + +
75B PHE* 1.3 60.3 + - + +
77B ALA* 3.4 6.2 + - - +
78B SER* 3.0 28.1 + - - -
452B GLU* 5.0 5.4 - - - +
513B THR* 3.8 16.1 - - + +
517B THR* 3.7 37.7 + - + +
726B LEU* 4.3 13.9 - - - -
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Residues in contact with PHE 75 (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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71B LEU* 2.8 40.5 + - + +
72B ALA 3.9 2.5 - - - +
74B LYS* 1.3 71.4 - - + +
76B ARG* 1.3 64.3 + - - +
78B SER* 2.9 19.8 + - - -
79B ARG* 3.1 15.7 + - - +
510B ILE* 3.5 44.4 - - + -
513B THR* 3.8 21.5 - - + -
514B PHE* 4.2 14.6 - + + -
708B VAL* 4.4 8.3 - - + -
711B ALA* 3.7 12.6 - - + -
712B ALA* 3.8 23.1 - - + -
715B TRP* 3.5 42.4 - + + -
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Residues in contact with ARG 76 (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 GLN* 5.9 1.8 + - - -
72B ALA* 2.9 32.8 + - - +
73B GLU* 3.8 25.7 + - - +
75B PHE* 1.3 77.1 - - - +
77B ALA* 1.3 62.4 + - - +
79B ARG* 3.2 13.3 + - - +
80B ASN* 3.2 13.4 + - - +
103B LEU* 3.9 25.7 - - + +
705B ASP* 6.2 2.4 - - - +
708B VAL* 3.9 25.6 - - + +
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Residues in contact with ALA 77 (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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73B GLU 3.2 15.8 + - - +
74B LYS* 3.8 3.4 - - - +
76B ARG* 1.3 79.9 - - - +
78B SER* 1.3 62.2 + - - +
80B ASN* 3.1 12.3 + - - +
451B ASN* 2.8 30.7 + - - +
452B GLU* 3.4 34.3 - - - +
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Residues in contact with SER 78 (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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74B LYS 3.0 12.2 + - - -
75B PHE* 2.9 16.0 + - - -
77B ALA* 1.3 77.2 - - - +
79B ARG* 1.3 57.1 + - - +
81B TYR* 3.1 24.1 - - - -
451B ASN 4.0 11.7 + - - +
452B GLU* 5.3 1.8 + - - -
453B LEU* 4.3 6.3 - - - +
509B PRO* 3.2 30.2 + - - +
510B ILE* 3.6 9.4 + - - +
513B THR* 3.2 25.1 + - - -
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Residues in contact with ARG 79 (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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75B PHE 3.1 14.5 + - - +
76B ARG* 3.8 1.8 - - - +
77B ALA 3.1 0.4 - - - -
78B SER* 1.3 80.6 + - - +
80B ASN* 1.3 56.2 + - - +
81B TYR* 3.0 7.2 + - - -
83B LYS* 2.8 33.2 + - - +
102B GLY 3.2 7.9 + - - +
103B LEU* 3.8 13.7 - - + +
509B PRO* 4.2 13.3 - - + +
510B ILE* 3.6 33.7 - - + +
704B THR* 4.3 20.5 + - - +
707B ASN* 5.5 12.0 - - - +
708B VAL* 3.9 17.7 - - - +
13D HIS 4.2 13.9 + - - -
14D VAL* 4.3 2.8 - - - +
15D ASP* 3.6 43.7 + - - +
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Residues in contact with ASN 80 (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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76B ARG 3.2 14.5 + - - +
77B ALA* 3.1 13.1 + - - +
78B SER 3.3 0.4 - - - -
79B ARG* 1.3 73.1 - - - +
81B TYR* 1.3 58.5 + - - +
101B ARG 4.7 3.1 - - - +
102B GLY* 4.3 7.9 - - - -
103B LEU* 3.7 30.0 + - + +
451B ASN* 3.4 25.7 + - - +
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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