Contacts of the helix formed by residues 64 - 79 (chain A) in PDB entry 1NLW
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 ILE 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA 3.0 21.5 + - - +
61A VAL* 3.6 9.0 - - + +
63A GLN* 1.3 76.5 - - - +
65A ASP* 1.3 56.8 + - - +
67A LEU* 3.2 4.1 + - - +
68A GLN* 2.9 57.4 + - - +
260B HIS* 4.0 32.8 - - + +
263B ASP* 4.0 26.7 - - + +
264B ILE* 3.5 17.7 - - + +
267B LEU* 4.1 13.7 - - + -
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Residues in contact with ASP 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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61A VAL* 3.2 12.4 + - + +
62A HIS* 3.5 12.3 - - - +
64A ILE* 1.3 81.6 - - - +
66A GLN* 1.3 75.9 + - - +
68A GLN* 3.3 14.9 + - - +
69A ARG* 2.6 66.2 + - - +
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Residues in contact with GLN 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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62A HIS* 3.0 50.1 + - + +
63A GLN* 3.2 8.9 + - - +
65A ASP* 1.3 97.7 + - - +
67A LEU* 1.3 59.8 + - + +
69A ARG* 3.3 17.7 + - - +
70A GLU* 2.9 29.2 + - - +
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Residues in contact with LEU 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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63A GLN* 2.7 29.1 + - + +
64A ILE* 3.6 4.5 - - - +
66A GLN* 1.3 73.4 - - + +
68A GLN* 1.3 53.1 + - - +
70A GLU* 3.3 25.7 + - - +
71A GLN* 2.8 30.3 + - - +
264B ILE* 3.7 42.4 - - + +
267B LEU* 3.9 23.3 - - + +
268B LYS* 4.0 22.4 - - + -
271B ASN* 3.1 14.5 + - - +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 2.9 41.4 + - - +
65A ASP* 3.6 14.5 - - - +
66A GLN 3.2 0.2 - - - -
67A LEU* 1.3 74.5 - - - +
69A ARG* 1.3 63.2 + - - +
71A GLN* 3.2 8.3 + - - +
72A ARG* 3.1 45.6 + - - +
267B LEU* 3.9 17.0 - - + +
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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
----------------------------------------------------------
65A ASP* 2.6 52.2 + - - +
66A GLN* 3.7 21.0 - - - +
68A GLN* 1.3 72.6 - - - +
70A GLU* 1.3 65.5 + - - +
72A ARG* 3.4 28.5 + - - +
73A HIS* 3.1 22.9 + - - +
76A ARG* 4.9 2.1 + - - -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN 2.9 18.3 + - - +
67A LEU* 3.4 19.5 - - - +
69A ARG* 1.3 78.0 - - - +
71A GLN* 1.3 61.3 + - - +
73A HIS* 3.4 6.7 + - - +
74A LEU* 3.1 31.3 + - + +
271B ASN* 2.8 32.1 + - - +
275B GLU* 5.2 6.8 - - - +
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Residues in contact with GLN 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 LEU 2.8 17.4 + - - +
68A GLN* 3.6 9.1 - - - +
69A ARG 3.2 0.4 - - - -
70A GLU* 1.3 74.0 - - - +
72A ARG* 1.3 64.2 + - + +
74A LEU* 3.1 6.9 + - - +
75A LYS* 3.0 39.8 + - + +
267B LEU* 4.5 8.5 + - - +
270B GLN* 3.1 40.4 + - - +
271B ASN* 3.1 29.3 + - - +
274B LEU* 4.2 12.6 - - + -
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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 GLN* 3.1 36.2 + - - +
69A ARG* 3.4 35.9 + - - +
71A GLN* 1.3 77.0 - - + +
73A HIS* 1.3 56.4 + - - +
75A LYS* 3.4 8.7 + - - +
76A ARG* 3.0 46.8 + - - +
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Residues in contact with HIS 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 ARG 3.1 12.4 + - - +
70A GLU* 3.6 11.0 - - - +
71A GLN 3.1 0.8 - - - -
72A ARG* 1.3 74.7 - - - +
74A LEU* 1.3 67.1 + - + +
76A ARG* 3.4 26.7 + - - +
77A GLN* 2.9 60.4 + - + +
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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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70A GLU* 3.1 18.6 + - + +
71A GLN 3.1 6.3 + - - +
73A HIS* 1.3 82.9 - - + +
75A LYS* 1.3 57.4 + - - +
77A GLN* 3.4 17.8 + - - +
78A LEU* 2.8 32.2 + - - +
271B ASN* 3.6 43.5 - - + +
274B LEU* 3.7 22.2 - - + -
275B GLU* 3.0 42.6 - - + +
278B VAL* 4.1 7.0 - - + +
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Residues in contact with LYS 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 GLN* 3.0 34.7 + - + +
72A ARG* 3.6 10.3 - - - +
74A LEU* 1.3 76.5 - - - +
76A ARG* 1.3 60.0 + - + +
78A LEU* 3.2 19.0 + - + +
79A GLU* 2.6 29.2 + - - +
274B LEU* 3.8 29.8 - - + +
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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 ARG 4.9 2.0 + - - -
72A ARG* 3.0 29.7 + - + +
73A HIS* 3.6 36.5 + - - +
75A LYS* 1.3 77.5 - - + +
77A GLN* 1.3 62.1 + - - +
79A GLU* 3.1 27.2 - - + +
80A LYS* 3.8 4.0 + - - +
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Residues in contact with GLN 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 HIS* 2.9 43.5 + - + +
74A LEU* 3.6 16.8 - - - +
76A ARG* 1.3 72.4 - - - +
78A LEU* 1.3 54.6 + - - +
79A GLU 2.8 14.1 + - - -
80A LYS* 2.8 25.0 + - + +
275B GLU* 5.0 0.5 - - - +
278B VAL* 3.5 29.5 - - + +
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Residues in contact with LEU 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 LEU 2.8 18.6 + - - +
75A LYS* 3.4 15.9 - - + +
77A GLN* 1.3 75.8 - - - +
79A GLU* 1.3 65.8 + - - +
80A LYS 3.7 5.6 - - - +
274B LEU* 4.7 12.6 - - + -
277B GLN* 3.5 51.8 - - + +
278B VAL* 3.3 26.2 - - + +
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Residues in contact with GLU 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 LYS* 2.6 25.7 + - - +
76A ARG* 3.1 23.3 - - + +
77A GLN 2.8 1.4 + - - -
78A LEU* 1.3 81.4 - - - +
80A LYS* 1.3 67.3 + - - +
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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