Contacts of the helix formed by residues 87 - 101 (chain A) in PDB entry 2NUN
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 SER 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ILE* 3.7 6.4 - - - +
86A THR* 1.3 81.9 + - - +
88A PHE* 1.3 64.0 + - - +
89A GLU* 3.7 8.6 + - - +
90A GLU* 3.2 26.8 + - - +
91A LEU* 3.2 17.3 + - - +
231A ASN* 3.8 13.2 - - - +
234A TYR* 3.6 13.8 - - - -
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Residues in contact with PHE 88 (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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87A SER* 1.3 68.7 - - - +
89A GLU* 1.3 57.4 + - - +
91A LEU* 2.8 10.9 + - + +
92A TRP* 2.7 72.3 + + + -
227A LYS* 5.3 4.5 - - + -
230A LEU* 3.7 56.3 - - + +
231A ASN* 2.8 22.0 - - - +
234A TYR* 3.8 23.0 - + + -
254A THR* 3.6 28.3 - - + -
258A ALA* 4.2 6.5 - - + -
263A PRO* 6.1 0.4 - - + -
275A ALA* 3.9 21.1 - - + -
279A ILE* 5.0 0.4 - - + -
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Residues in contact with GLU 89 (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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87A SER* 3.9 9.6 + - - +
88A PHE* 1.3 83.3 - - - +
90A GLU* 1.3 56.6 + - - +
92A TRP* 3.6 9.6 + - - +
93A GLY* 3.1 22.0 + - - -
227A LYS* 6.1 9.0 - - + -
231A ASN* 3.3 15.2 - - - +
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Residues in contact with GLU 90 (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 SER* 5.6 2.0 - - - -
84A GLY 3.1 22.5 - - - +
85A ILE* 3.5 12.3 - - + +
86A THR* 3.0 33.7 + - - +
87A SER* 3.2 19.7 + - - +
88A PHE 3.0 0.6 - - - -
89A GLU* 1.3 77.5 - - - +
91A LEU* 1.3 67.0 + - - +
93A GLY* 3.1 3.0 + - - -
94A ARG* 3.0 33.0 + - - +
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Residues in contact with LEU 91 (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 ALA* 4.1 7.9 - - + -
80A ILE* 4.0 12.6 - - + -
85A ILE* 3.7 28.0 - - + +
87A SER 3.2 8.7 + - - +
88A PHE* 2.8 12.5 + - + +
90A GLU* 1.3 76.6 - - - +
92A TRP* 1.3 59.8 + - - +
94A ARG* 3.0 3.1 + - + +
95A ALA* 2.8 26.7 + - - +
234A TYR* 4.1 8.3 - - + -
274A PHE* 4.4 6.7 - - + -
275A ALA* 3.7 36.8 - - + +
278A ALA* 3.7 20.6 - - + -
279A ILE* 3.8 21.1 - - + -
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Residues in contact with TRP 92 (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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88A PHE* 2.7 46.3 + + + +
89A GLU* 3.7 9.2 - - - +
91A LEU* 1.3 74.1 - - - +
93A GLY* 1.3 58.3 + - - +
95A ALA* 3.3 5.5 + - - +
96A THR* 2.8 38.6 + - - -
116A GLU* 5.8 1.5 + - - -
227A LYS* 6.4 1.6 - - + -
258A ALA* 4.1 13.2 - - + -
263A PRO* 3.6 41.1 - - + +
264A ASP* 2.7 38.1 + - - -
268A SER* 3.8 13.0 - - - -
271A LYS* 3.5 37.5 - - + -
272A ALA* 3.6 16.8 - - - -
275A ALA* 5.0 1.3 - - + -
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Residues in contact with GLY 93 (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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89A GLU 3.1 13.8 + - - -
90A GLU* 3.1 4.9 + - - -
91A LEU 3.1 0.6 - - - -
92A TRP* 1.3 76.7 - - - +
94A ARG* 1.3 66.0 + - - +
96A THR* 3.3 5.9 + - - -
97A GLU* 3.0 34.0 + - - +
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Residues in contact with ARG 94 (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 SER 5.7 0.4 - - - +
76A ALA* 4.3 18.8 - - + -
79A GLU* 2.8 39.7 + - - -
84A GLY 5.2 0.6 + - - -
85A ILE* 4.1 17.3 - - + +
90A GLU* 3.0 24.6 + - - +
91A LEU* 3.6 8.1 - - + +
93A GLY* 1.3 77.3 - - - +
95A ALA* 1.3 62.4 + - - +
97A GLU* 3.5 17.2 + - - +
98A TRP* 3.1 23.5 + - + +
274A PHE* 4.3 8.2 - - + -
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Residues in contact with ALA 95 (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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91A LEU 2.8 13.1 + - - +
92A TRP* 3.5 12.1 - - - +
94A ARG* 1.3 79.7 - - - +
96A THR* 1.3 58.9 + - - +
98A TRP* 3.4 6.1 + - - +
99A ARG* 3.1 23.4 + - - +
271A LYS* 3.9 27.7 - - + +
274A PHE* 3.5 35.6 - - + -
275A ALA* 4.9 0.9 - - + +
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Residues in contact with THR 96 (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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92A TRP* 2.8 25.0 + - - -
93A GLY* 3.3 7.6 + - - -
95A ALA* 1.3 77.4 - - - +
97A GLU* 1.3 59.1 + - + +
99A ARG* 3.1 2.8 + - - +
100A LEU* 2.8 42.1 + - + +
113A PHE 3.5 23.8 - - - +
114A ALA* 4.0 12.1 - - + +
264A ASP* 3.7 6.8 + - - +
271A LYS* 3.5 24.0 - - - +
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Residues in contact with GLU 97 (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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93A GLY* 3.0 22.3 + - - +
94A ARG* 4.1 18.9 + - - +
96A THR* 1.3 77.6 - - + +
98A TRP* 1.3 62.3 + - - +
100A LEU* 3.5 14.7 + - + +
101A SER* 3.2 21.3 + - - -
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Residues in contact with TRP 98 (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 TYR* 3.5 46.0 - + - -
68A SER* 2.8 26.6 + - - -
69A MET* 3.3 44.4 - - + -
72A SER* 3.1 24.7 - - - +
94A ARG* 3.1 18.8 + - + +
95A ALA 3.7 6.1 - - - +
96A THR 3.2 0.2 - - - -
97A GLU* 1.3 75.5 - - - +
99A ARG* 1.3 93.3 + - + +
101A SER* 2.5 27.7 + - - -
102A LYS* 3.5 21.7 + - + +
270A ALA* 4.5 6.5 - - + -
271A LYS* 6.5 0.2 - - - -
274A PHE* 3.9 25.6 - + + -
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Residues in contact with ARG 99 (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 TYR* 2.8 36.8 + - - -
95A ALA 3.1 14.2 + - - +
96A THR* 3.4 11.0 - - - +
98A TRP* 1.3 89.3 - - + +
100A LEU* 1.3 62.6 + - - +
102A LYS* 3.1 18.6 + - - +
103A LEU* 3.9 15.5 + - - +
113A PHE* 3.8 43.9 - - + +
267A GLY* 5.0 0.4 - - - -
270A ALA* 3.9 18.0 - - + +
271A LYS* 4.3 16.4 - - + -
600A ADP 3.3 36.8 + - - -
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Residues in contact with LEU 100 (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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96A THR* 2.8 35.2 + - + +
97A GLU* 3.9 13.5 - - + +
98A TRP 3.3 0.2 - - - -
99A ARG* 1.3 73.3 - - - +
101A SER* 1.3 61.6 + - - +
102A LYS 3.1 0.7 - - - -
103A LEU* 3.2 27.5 + - + +
110A TYR* 3.4 65.9 - - + +
113A PHE* 3.7 18.4 - - + +
114A ALA* 3.6 22.2 - - + +
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Residues in contact with SER 101 (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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97A GLU 3.2 12.5 + - - -
98A TRP* 2.5 27.0 + - - -
100A LEU* 1.3 76.6 - - - +
102A LYS* 1.3 73.8 + - - +
103A LEU 3.3 4.6 + - - +
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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