Contacts of the helix formed by residues 63 - 79 (chain A) in PDB entry 3NPC
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 ASN 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE 2.9 4.8 + - - +
62A GLN* 1.3 85.9 + - - +
64A GLN* 1.3 58.6 + - - +
65A THR* 2.9 11.3 + - - -
66A HIS* 2.8 54.3 + - - +
67A ALA* 3.0 30.6 + - - +
349A ILE* 4.4 9.4 - - - -
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Residues in contact with GLN 64 (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 ASN* 1.3 75.2 - - - +
65A THR* 1.3 62.7 + - - +
67A ALA* 3.8 5.0 - - - +
68A LYS* 3.2 26.7 + - - +
346A GLU* 5.1 7.1 - - - +
347A HIS 2.6 28.6 + - - +
348A ALA* 4.1 2.2 - - - +
349A ILE* 3.9 20.6 - - + +
352A TRP* 3.0 27.1 + - - +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 2.9 9.8 + - - -
64A GLN* 1.3 76.8 - - - +
66A HIS* 1.3 69.0 + - + +
68A LYS* 4.1 3.1 - - - +
69A ARG* 3.4 61.5 + - - +
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Residues in contact with HIS 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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36A ALA* 3.2 36.7 + - + +
37A GLN* 4.4 11.4 + - + +
58A SER 5.0 3.2 + - - -
60A PRO* 2.9 21.4 - - + +
62A GLN* 3.9 31.6 + - + -
63A ASN* 2.8 47.1 + - - +
65A THR* 1.3 78.0 - - + +
67A ALA* 1.3 57.4 + - - +
69A ARG* 3.3 6.6 + - - +
70A ALA* 3.0 28.8 + - - +
173A ALA* 6.5 0.2 - - + -
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Residues in contact with ALA 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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60A PRO 2.7 16.2 + - - +
61A PHE* 4.0 7.2 - - - +
63A ASN 3.0 16.4 + - - +
64A GLN 3.8 2.0 - - - +
65A THR 3.3 0.2 - - - -
66A HIS* 1.3 75.5 - - - +
68A LYS* 1.3 58.2 + - - +
70A ALA 3.4 0.9 + - - -
71A TYR* 3.0 30.7 + - - +
352A TRP* 3.5 42.1 - - + -
356A ILE* 3.7 8.3 - - + +
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Residues in contact with LYS 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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64A GLN 3.2 15.4 + - - +
65A THR* 4.1 4.5 - - - +
67A ALA* 1.3 78.2 - - - +
69A ARG* 1.3 58.9 + - + +
71A TYR* 4.0 0.7 - - - +
72A ARG* 2.9 41.7 + - - +
343A GLU* 3.1 50.4 + - + +
344A GLU* 3.1 30.8 + - - +
352A TRP* 3.8 21.7 - - + -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 5.0 20.2 - - + +
65A THR* 3.4 42.5 + - - +
66A HIS* 3.3 6.2 + - - +
67A ALA 3.2 0.6 - - - -
68A LYS* 1.3 78.8 - - + +
70A ALA* 1.3 58.9 + - - +
72A ARG* 3.8 26.6 - - - +
73A GLU* 3.1 29.5 + - - +
173A ALA* 4.3 20.2 - - - +
365A B96 3.5 21.6 - - + +
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Residues in contact with ALA 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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57A LEU* 4.1 23.0 - - + +
60A PRO* 3.2 37.0 - - + -
66A HIS 3.0 10.9 + - - +
67A ALA 3.7 3.8 - - - +
69A ARG* 1.3 76.8 - - - +
71A TYR* 1.3 61.3 + - - +
73A GLU* 3.4 4.1 + - - +
74A LEU* 3.2 29.9 + - - +
356A ILE* 4.0 9.0 - - + -
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Residues in contact with TYR 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 ALA 3.0 18.1 + - - +
68A LYS 4.0 0.7 - - - +
70A ALA* 1.3 75.1 - - - +
72A ARG* 1.3 66.4 + - - +
74A LEU* 3.3 5.0 + - - +
75A VAL* 3.0 51.0 + - + +
78A LYS* 5.4 1.7 + - - -
342A LEU* 3.6 30.2 - - + +
343A GLU* 3.9 32.3 - - + -
352A TRP* 3.8 22.9 - + + -
355A LEU* 4.0 39.4 - - + +
356A ILE* 4.1 13.0 - - + +
359A GLU* 3.9 19.2 + - + -
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Residues in contact with ARG 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 LYS* 2.9 38.6 + - - +
69A ARG* 3.8 29.0 - - - +
71A TYR* 1.3 77.9 - - - +
73A GLU* 1.3 56.7 + - - +
75A VAL* 3.3 5.0 + - - +
76A LEU* 2.9 53.5 + - + +
338A TYR* 3.7 16.2 - - + +
343A GLU* 2.9 40.1 + - - +
365A B96 4.0 19.7 - - + +
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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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37A GLN* 4.1 2.4 - - - +
55A LYS* 2.8 30.4 + - - -
57A LEU* 3.8 13.6 - - + +
69A ARG 3.1 18.3 + - - +
70A ALA 3.8 5.4 - - - +
71A TYR 3.3 0.2 - - - -
72A ARG* 1.3 75.4 - - - +
74A LEU* 1.3 63.9 + - + +
76A LEU* 4.0 0.5 - - - +
77A LEU* 3.1 38.7 + - + +
106A LEU* 3.7 19.0 - - + +
365A B96 2.8 62.4 + - + +
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Residues in contact with LEU 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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57A LEU* 5.3 3.8 - - + -
70A ALA 3.2 17.7 + - - +
71A TYR* 3.8 6.1 - - - +
73A GLU* 1.3 78.4 - - + +
75A VAL* 1.3 61.1 + - - +
77A LEU* 3.7 5.8 + - - +
78A LYS* 3.2 22.3 + - - +
88A LEU* 5.5 3.0 - - + +
91A VAL* 4.0 18.6 - - + -
104A VAL* 4.4 8.5 - - + -
106A LEU* 3.8 29.2 - - + -
356A ILE* 3.9 31.0 - - + +
359A GLU* 3.7 34.8 - - + +
360A VAL* 4.4 7.0 - - + -
363A TRP* 6.0 2.9 - - + -
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Residues in contact with VAL 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 TYR* 3.0 57.9 + - + +
72A ARG* 4.0 3.1 - - - +
74A LEU* 1.3 74.4 - - - +
76A LEU* 1.3 64.7 + - - +
78A LYS* 3.2 34.7 + - - +
79A CYS* 3.3 13.4 - - - -
338A TYR* 3.7 27.8 - - + -
339A ASP 4.8 7.0 - - - +
359A GLU* 3.8 15.3 - - - +
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Residues in contact with LEU 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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72A ARG* 2.9 45.4 + - + +
73A GLU* 4.0 2.9 - - - +
75A VAL* 1.3 75.0 - - - +
77A LEU* 1.3 57.8 + - + +
79A CYS* 3.0 22.6 + - - +
80A VAL* 3.6 13.1 + - - +
147A ILE* 3.6 35.8 - - + +
338A TYR* 3.6 33.7 - - + -
365A B96 3.7 40.8 - - + +
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Residues in contact with LEU 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 47.5 + - + +
74A LEU* 4.1 3.8 - - - +
76A LEU* 1.3 75.6 - - - +
78A LYS* 1.3 60.1 + - - +
79A CYS 3.3 0.2 - - - -
80A VAL* 3.6 22.6 + - + +
86A ILE* 3.7 44.9 - - + +
87A SER* 5.8 0.2 - - - -
88A LEU* 3.7 41.0 + - + +
106A LEU* 4.4 5.6 - - + -
363A TRP* 5.9 1.4 + - - -
365A B96 3.8 21.3 - - + +
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Residues in contact with LYS 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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71A TYR* 5.4 1.4 + - - -
74A LEU 3.2 13.0 + - - +
75A VAL* 3.2 35.4 + - - +
77A LEU* 1.3 78.4 - - - +
79A CYS* 1.3 60.4 + - - +
80A VAL 3.4 2.6 + - - +
335A PRO* 3.7 13.2 - - - +
336A GLN* 4.2 26.9 + - - +
359A GLU* 2.9 31.3 + - - +
363A TRP* 6.2 6.7 - - + +
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Residues in contact with CYS 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 VAL* 3.3 20.4 - - - -
76A LEU 3.0 9.8 + - - +
78A LYS* 1.3 81.5 - - - +
80A VAL* 1.3 58.1 + - - +
145A ALA* 4.0 1.8 - - + +
147A ILE* 4.4 12.3 - - + -
334A PRO* 3.4 13.5 - - - +
335A PRO* 3.1 22.5 - - - +
336A GLN* 3.6 31.9 - - - +
337A ILE 4.6 0.4 - - - -
338A TYR* 3.8 33.0 - - - +
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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