Contacts of the helix formed by residues 66 - 80 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ASP 5.4 1.6 - - - -
64A GLN 3.7 5.0 + - - +
65A ASN* 1.4 72.2 + - - +
67A ASP* 1.3 65.7 + - - +
68A ILE 3.2 1.4 + - - -
69A GLN* 3.5 14.2 + - - +
70A LYS* 3.9 22.7 + - - +
720A ARG* 4.6 3.0 - - - +
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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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65A ASN* 3.0 13.8 + - - +
66A ALA* 1.3 81.1 - - - +
68A ILE* 1.3 58.1 + - - +
69A GLN 3.2 0.2 - - - -
70A LYS* 3.1 11.8 + - - +
71A LEU* 2.9 30.1 + - + +
518A TYR* 4.4 9.5 + - - +
716A GLY* 6.2 1.3 - - - -
720A ARG* 5.1 6.5 + - - -
724A LEU 4.6 5.7 - - - +
725A GLU* 4.3 10.7 - - - +
726A LEU* 3.4 44.8 + - + +
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Residues in contact with ILE 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 LEU* 3.7 52.7 - - + +
65A ASN* 3.7 28.7 - - + +
66A ALA 3.2 1.0 - - - -
67A ASP* 1.3 77.2 - - - +
69A GLN* 1.3 57.6 + - - +
71A LEU* 3.1 7.0 + - - +
72A ALA* 2.9 25.8 + - + +
709A LYS* 6.3 0.7 - - + -
712A ALA* 3.5 27.9 - - + +
713A ASP* 3.4 25.8 - - - +
716A GLY* 4.0 6.3 - - - -
717A PHE 4.7 0.2 - - - +
801A GOL 3.4 16.4 - - - +
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Residues in contact with GLN 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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66A ALA* 3.5 10.7 + - - +
67A ASP 3.2 0.4 - - - -
68A ILE* 1.3 79.8 - - - +
70A LYS* 1.3 64.3 + - + +
72A ALA* 3.4 14.8 + - - +
73A GLU* 3.1 39.2 + - - +
76A ARG* 5.4 3.3 + - - -
801A GOL 3.5 19.0 + - - +
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Residues in contact with LYS 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 ALA* 3.9 21.8 + - - +
67A ASP* 3.1 15.4 + - - +
69A GLN* 1.3 79.7 - - + +
71A LEU* 1.3 62.9 + - - +
73A GLU* 3.2 20.1 + - - +
74A LYS* 3.1 33.7 + - - +
726A LEU* 3.4 30.1 - - + -
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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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67A ASP 2.9 19.0 + - - +
68A ILE* 3.1 7.4 + - - +
70A LYS* 1.3 73.6 - - - +
72A ALA* 1.3 61.0 + - - +
74A LYS* 3.2 10.8 + - + +
75A PHE* 2.8 65.2 + - + -
514A PHE* 4.8 0.4 - - + -
517A THR* 4.4 14.4 - - + -
518A TYR* 3.7 35.9 - - + +
712A ALA* 4.2 4.9 - - + +
715A TRP* 4.0 5.2 - - + -
716A GLY* 3.6 37.2 - - - +
726A LEU* 4.7 3.8 - - + -
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Residues in contact with ALA 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 ILE* 2.9 14.0 + - + +
69A GLN* 3.5 22.7 - - - +
70A LYS 3.3 0.2 - - - -
71A LEU* 1.3 76.9 - - - +
73A GLU* 1.3 58.1 + - + +
75A PHE* 4.5 0.2 - - - -
76A ARG* 2.9 46.6 + - - +
708A VAL* 3.7 13.2 - - + +
709A LYS* 5.3 5.2 - - + -
712A ALA* 3.5 18.3 - - + +
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Residues in contact with GLU 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 GLN* 3.1 30.8 + - - +
70A LYS* 3.5 19.2 - - - +
71A LEU 3.2 0.2 - - - -
72A ALA* 1.3 76.2 - - + +
74A LYS* 1.3 65.7 + - + +
76A ARG* 3.9 19.3 + - - +
77A ALA* 3.1 23.6 + - - +
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Residues in contact with LYS 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 LYS* 3.1 21.6 + - - +
71A LEU* 3.8 13.2 - - + +
73A GLU* 1.3 78.7 - - + +
75A PHE* 1.3 60.6 + - + +
77A ALA* 3.4 7.0 + - - +
78A SER* 3.0 27.4 + - - -
452A GLU* 4.9 5.8 - - - +
513A THR* 3.8 16.4 - - + +
517A THR* 3.7 35.9 + - + +
726A LEU* 4.4 12.8 - - - -
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Residues in contact with PHE 75 (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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71A LEU* 2.8 43.9 + - + +
72A ALA 3.9 2.2 - - - +
74A LYS* 1.3 71.3 - - + +
76A ARG* 1.3 66.3 + - - +
78A SER* 2.9 20.5 + - - -
79A ARG* 3.1 14.9 + - - +
510A ILE* 3.6 43.3 - - + -
513A THR* 3.9 20.4 - - + -
514A PHE* 4.2 9.9 - + + -
708A VAL* 4.3 8.1 - - + -
711A ALA* 3.6 11.9 - - + -
712A ALA* 3.7 24.5 - - + -
715A TRP* 3.5 43.1 - + + -
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Residues in contact with ARG 76 (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 GLN* 5.4 3.0 + - - -
72A ALA* 2.9 34.7 + - - +
73A GLU* 3.9 23.1 + - - +
75A PHE* 1.3 76.1 - - - +
77A ALA* 1.3 63.5 + - - +
79A ARG* 3.2 5.5 + - - +
80A ASN* 3.1 20.9 + - + +
103A LEU* 4.0 25.5 - - + +
705A ASP* 6.1 3.4 - - - +
708A VAL* 3.8 25.4 - - + +
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Residues in contact with ALA 77 (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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73A GLU 3.1 15.0 + - - +
74A LYS* 3.7 5.4 - - - +
75A PHE 3.3 0.2 - - - -
76A ARG* 1.3 79.9 - - - +
78A SER* 1.3 63.1 + - - +
80A ASN* 3.1 13.0 + - - +
451A ASN* 2.9 29.7 + - - +
452A GLU* 3.5 31.9 - - - +
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Residues in contact with SER 78 (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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74A LYS 3.0 13.0 + - - -
75A PHE* 2.9 15.5 + - - -
77A ALA* 1.3 76.9 - - - +
79A ARG* 1.3 56.4 + - - +
81A TYR* 3.2 23.7 - - - -
450A VAL* 5.4 0.2 - - - +
451A ASN 4.1 13.5 + - - +
452A GLU* 5.2 1.5 + - - -
453A LEU* 4.3 6.2 - - - +
509A PRO* 3.2 30.9 + - - +
510A ILE* 3.6 8.7 + - - +
513A THR* 3.2 24.6 + - - -
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Residues in contact with ARG 79 (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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75A PHE 3.1 14.8 + - - +
76A ARG* 3.2 7.2 + - - +
78A SER* 1.3 79.6 - - - +
80A ASN* 1.3 55.8 + - - +
81A TYR* 3.0 6.0 + - - -
83A LYS* 2.8 32.2 + - - +
102A GLY 3.3 6.2 + - - +
103A LEU* 3.8 14.3 - - + +
509A PRO* 3.8 21.4 - - - +
510A ILE* 4.0 29.8 - - + +
704A THR* 4.6 18.3 + - - +
707A ASN* 5.1 16.5 - - - +
708A VAL* 4.7 9.4 - - + +
13C HIS 4.1 17.4 + - - -
14C VAL* 4.5 2.2 - - - +
15C ASP* 4.2 33.4 + - - +
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Residues in contact with ASN 80 (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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76A ARG* 3.1 14.4 + - + +
77A ALA* 3.1 13.1 + - - +
78A SER 3.4 0.2 - - - -
79A ARG* 1.3 72.4 - - - +
81A TYR* 1.3 59.2 + - - +
101A ARG 4.7 2.6 - - - +
102A GLY* 4.3 6.9 - - - -
103A LEU* 3.6 31.1 + - + +
451A ASN* 3.3 26.7 - - - +
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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