Contacts of the helix formed by residues 57 - 73 (chain A) in PDB entry 1NM8
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 GLY 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU 5.2 2.2 - - - -
52A PHE 4.8 2.0 - - - -
54A ALA* 2.9 22.3 + - - -
55A SER 3.1 1.3 - - - -
56A GLY* 1.3 83.2 - - - +
58A VAL* 1.3 65.5 + - - -
59A GLY 3.4 2.6 + - - -
60A GLU* 3.5 5.0 + - - +
61A ARG* 3.3 20.0 + - - +
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Residues in contact with VAL 58 (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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51A GLU 5.3 1.6 + - - -
52A PHE* 3.9 18.3 + - + +
57A GLY* 1.3 68.3 - - - -
59A GLY* 1.3 67.1 + - - +
61A ARG* 3.1 11.2 + - + +
62A LEU* 3.0 44.5 + - + +
511A VAL* 5.3 10.1 - - + -
512A SER 6.0 0.7 - - - +
514A PRO* 4.5 10.1 - - + -
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Residues in contact with GLY 59 (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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22A LEU* 3.6 12.8 - - - +
52A PHE* 2.9 51.3 + - - -
58A VAL* 1.3 76.0 - - - +
60A GLU* 1.3 57.1 + - - +
62A LEU* 3.3 2.3 + - - +
63A GLN* 2.9 29.8 + - - +
502A LEU* 4.7 0.5 - - - +
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Residues in contact with GLU 60 (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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22A LEU* 3.8 12.3 - - + +
23A GLN* 5.9 1.2 + - - -
52A PHE 4.4 0.4 + - - -
53A GLN 4.5 6.7 - - - +
54A ALA 4.1 9.4 - - - +
55A SER* 3.7 13.9 + - - -
56A GLY* 2.8 31.4 + - - -
57A GLY 3.5 6.8 + - - +
58A VAL 3.3 0.4 - - - -
59A GLY* 1.3 76.1 - - - +
61A ARG* 1.3 62.7 + - - +
63A GLN* 3.4 7.8 + - - +
64A LYS* 3.0 23.9 + - - +
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Residues in contact with ARG 61 (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 GLY 3.3 9.8 + - - +
58A VAL* 3.1 14.2 + - - +
60A GLU* 1.3 80.5 - - - +
62A LEU* 1.3 66.0 + - + +
64A LYS* 3.4 6.5 + - - +
65A GLY* 3.1 18.0 + - - -
68A ARG* 5.4 1.9 + - - -
509A ASP* 3.4 45.7 + - - +
511A VAL* 4.3 18.6 - - - +
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Residues in contact with LEU 62 (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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52A PHE* 4.0 18.4 - - + -
58A VAL* 3.0 36.1 + - + +
59A GLY 3.8 3.8 - - - +
61A ARG* 1.3 80.7 - - + +
63A GLN* 1.3 66.8 + - - +
65A GLY* 3.1 2.4 + - - -
66A LEU* 3.0 22.0 + - - +
502A LEU* 3.5 31.9 - - + +
505A GLN* 3.6 17.7 - - + +
506A ALA* 3.5 37.9 - - + +
509A ASP* 4.8 7.0 - - + -
511A VAL* 4.4 8.3 - - + -
514A PRO* 4.4 4.9 - - + -
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Residues in contact with GLN 63 (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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19A VAL* 3.6 14.2 + - - +
20A PRO 3.0 23.7 + - - -
21A PRO* 4.2 2.4 - - - +
22A LEU* 3.8 27.1 - - + +
59A GLY 2.9 18.0 + - - +
60A GLU* 3.6 8.7 - - - +
62A LEU* 1.3 75.8 - - - +
64A LYS* 1.3 65.3 + - - +
66A LEU* 3.2 4.9 + - - +
67A GLU* 3.0 51.8 + - - +
498A HIS* 2.8 27.5 + - - -
502A LEU* 3.9 5.8 - - + +
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Residues in contact with LYS 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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60A GLU 3.0 17.1 + - - +
61A ARG* 3.8 6.7 - - - +
63A GLN* 1.3 75.8 - - - +
65A GLY* 1.3 62.2 + - - +
67A GLU* 3.4 17.0 + - - +
68A ARG* 3.0 48.8 + - - +
71A ARG* 3.0 42.4 - - - +
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Residues in contact with GLY 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 ARG 3.1 10.5 + - - -
62A LEU 3.1 7.5 + - - -
63A GLN 3.1 1.0 - - - -
64A LYS* 1.3 78.4 - - - +
66A LEU* 1.3 55.0 + - - +
68A ARG* 3.3 26.9 + - - +
69A ARG* 3.0 26.7 + - - +
505A GLN* 3.7 20.7 + - - +
509A ASP* 6.1 0.2 - - - -
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Residues in contact with LEU 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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19A VAL* 3.9 19.8 - - + +
62A LEU 3.0 15.5 + - - +
63A GLN* 3.2 6.3 + - - +
65A GLY* 1.3 73.0 - - - +
67A GLU* 1.3 61.9 + - - +
69A ARG* 3.1 7.4 + - - +
70A ALA* 2.9 29.5 + - - +
76A TRP* 4.2 16.0 - - + +
80A TRP* 3.6 22.2 - - + -
498A HIS* 3.8 21.3 - - + +
501A GLY* 3.6 22.0 - - - +
502A LEU* 3.5 35.2 - - + +
505A GLN* 3.9 9.6 - - + +
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Residues in contact with GLU 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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19A VAL* 4.5 12.3 - - + +
21A PRO* 5.9 0.5 - - - +
63A GLN* 3.0 44.2 + - - +
64A LYS* 3.8 20.6 + - - +
66A LEU* 1.3 76.5 - - - +
68A ARG* 1.3 61.9 + - - +
70A ALA* 3.4 9.4 + - - +
71A ARG* 3.3 40.1 + - - +
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Residues in contact with ARG 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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61A ARG 5.4 1.2 + - - -
64A LYS* 3.0 48.0 + - - +
65A GLY* 3.4 26.2 + - - +
67A GLU* 1.3 74.7 - - - +
69A ARG* 1.3 64.5 + - - +
71A ARG* 3.0 31.9 + - - +
72A LYS* 3.3 38.0 + - + +
505A GLN* 4.4 8.9 - - - +
509A ASP* 5.0 5.5 + - - -
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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
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65A GLY 3.0 14.3 + - - +
66A LEU* 3.3 11.2 - - - +
68A ARG* 1.3 77.7 - - - +
70A ALA* 1.3 56.9 + - - +
72A LYS* 3.0 22.3 + - - +
73A THR* 2.9 36.3 + - + +
76A TRP* 3.0 31.9 + - + +
79A GLU* 4.4 20.2 + - - +
80A TRP* 3.3 57.2 - - - +
505A GLN* 4.4 3.1 - - - +
508A GLU* 3.3 30.7 + - - -
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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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16A ARG* 3.5 15.3 + - + -
17A LEU 4.8 5.4 - - - +
18A PRO* 6.3 0.2 - - + -
19A VAL* 4.2 13.9 - - + +
66A LEU 2.9 15.4 + - - +
67A GLU* 3.6 7.6 - - - +
68A ARG 3.2 0.2 - - - -
69A ARG* 1.3 77.1 - - - +
71A ARG* 1.3 60.7 + - - +
73A THR* 3.4 16.3 - - - +
76A TRP* 3.8 22.6 - - + +
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Residues in contact with ARG 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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16A ARG* 4.1 13.1 + - - +
64A LYS* 3.0 37.4 - - - +
67A GLU* 3.3 29.3 + - - +
68A ARG* 3.0 20.2 + - + +
70A ALA* 1.3 78.4 - - - +
72A LYS* 1.3 63.1 + - + +
73A THR 3.6 0.2 - - - -
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Residues in contact with LYS 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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16A ARG* 5.7 0.2 - - - -
68A ARG* 3.5 40.6 - - + +
69A ARG* 3.0 10.1 + - - +
71A ARG* 1.3 82.6 - - + +
73A THR* 1.3 66.7 + - + +
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Residues in contact with THR 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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16A ARG* 3.6 12.8 + - - -
69A ARG* 2.9 35.9 + - + +
70A ALA* 3.4 13.7 - - - +
71A ARG 3.6 0.2 - - - -
72A LYS* 1.3 86.9 - - + +
74A GLU* 1.3 63.9 + - - +
75A ASN* 3.9 9.8 - - - +
76A TRP* 3.2 23.3 + - - +
79A GLU* 5.4 10.5 - - - +
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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