Contacts of the helix formed by residues 76 - 91 (chain B) in PDB entry 2NLA
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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ASP* 3.6 9.9 - - - -
74B GLU 3.9 3.0 + - - +
75B CYS* 1.3 66.8 - - - +
77B GLN* 1.3 55.7 + - - +
78B LEU 3.5 1.6 - - - -
79B ARG* 3.4 35.5 + - + +
80B ARG* 3.0 46.3 + - + +
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ALA* 3.5 30.9 + - - +
230A GLY* 5.3 3.2 - - - -
231A MET* 3.6 36.5 - - - +
234A LYS* 6.3 0.8 - - - +
73B ASP* 2.9 8.4 + - - +
75B CYS* 2.5 30.6 + - + +
76B ALA* 1.3 70.6 - - - +
78B LEU* 1.3 58.4 + - - +
80B ARG* 3.3 9.1 + - - +
81B ILE* 2.9 41.2 + - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 4.5 3.1 - - + -
231A MET* 4.1 20.0 - - + -
235A LEU* 6.4 0.7 - - + -
246A LEU* 5.2 1.1 - - + -
249A VAL* 4.1 25.8 - - + -
250A MET* 4.8 4.7 - - + -
253A VAL* 4.0 14.6 - - + +
263A ARG* 5.2 0.9 - - - -
266A THR* 3.9 28.0 - - + +
267A LEU* 4.3 21.2 - - + +
270A PHE* 4.0 41.5 - - + -
73B ASP* 3.2 9.5 + - - +
77B GLN* 1.3 76.0 - - - +
79B ARG* 1.3 67.4 + - - +
81B ILE* 4.5 4.0 - - - +
82B GLY* 2.8 20.4 + - - -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A HIS* 3.6 22.2 + - - -
253A VAL* 3.1 33.3 + - + +
255A SER* 3.5 22.4 + - - -
256A ASP* 3.3 31.8 + - - +
263A ARG* 3.2 25.6 + - - +
73B ASP* 4.7 0.4 + - - -
76B ALA* 3.4 29.9 + - + +
77B GLN 3.3 0.6 - - - -
78B LEU* 1.3 75.4 - - - +
80B ARG* 1.3 56.0 + - - +
82B GLY* 2.8 7.6 + - - -
83B ASP* 2.7 38.6 + - - +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B CYS* 6.5 0.4 - - - -
76B ALA* 3.0 37.1 + - + +
77B GLN* 3.7 7.9 - - - +
79B ARG* 1.3 78.2 - - + +
81B ILE* 1.3 59.1 + - - +
83B ASP* 3.6 10.1 + - - +
84B LYS* 3.0 64.1 + - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL* 4.8 0.2 - - + -
224A HIS* 3.5 42.4 - - + +
227A ALA* 3.9 28.7 - - + -
228A PHE* 4.1 19.7 - - + -
231A MET* 4.8 2.9 - - + -
266A THR* 3.8 19.1 - - + +
77B GLN* 2.9 32.8 + - - +
78B LEU* 4.0 5.4 - - - +
80B ARG* 1.3 73.7 - - + +
82B GLY* 1.3 67.6 + - - +
84B LYS* 2.9 14.1 + - + +
85B VAL* 2.8 24.0 + - + +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A GLY* 3.3 10.4 - - - -
263A ARG* 3.4 25.0 + - - -
266A THR* 3.4 17.3 + - - -
78B LEU 2.8 10.8 + - - -
79B ARG 2.8 8.3 + - - -
81B ILE* 1.3 75.2 - - - +
83B ASP* 1.3 58.3 + - - +
85B VAL 3.4 0.2 + - - -
86B ASN* 2.9 24.3 + - - +
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A VAL* 4.4 2.1 - - - +
260A ASN* 3.6 14.2 + - - +
263A ARG* 2.8 43.6 + - - -
79B ARG* 2.7 23.3 + - - +
80B ARG* 4.0 8.8 - - - +
81B ILE 3.1 0.2 - - - -
82B GLY* 1.3 73.6 - - - +
84B LYS* 1.3 51.8 + - - +
86B ASN* 3.4 5.7 + - - +
87B LEU* 2.7 34.0 + - - +
90B LYS* 5.5 0.5 + - - -
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A HIS* 5.1 13.0 - - + +
80B ARG* 3.0 58.4 + - - +
81B ILE* 2.9 18.1 + - + +
83B ASP* 1.3 74.1 - - - +
85B VAL* 1.3 59.2 + - - +
87B LEU* 3.1 11.7 + - + +
88B ARG* 2.9 39.5 + - + +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A VAL* 6.1 0.4 - - + -
220A VAL* 4.0 16.2 - - + -
224A HIS* 3.8 26.7 - - + -
262A GLY* 3.6 17.5 - - - -
265A VAL* 3.7 18.2 - - + -
266A THR* 3.6 13.9 - - - +
319A PHE* 4.1 12.3 - - + -
81B ILE* 2.8 21.1 + - + +
82B GLY 3.7 3.8 - - - +
84B LYS* 1.3 71.8 - - - +
86B ASN* 1.3 62.1 + - - +
88B ARG* 3.8 6.1 + - - +
89B GLN* 3.4 23.9 + - - +
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASN* 3.1 48.8 - - - +
261A TRP 3.5 1.2 + - - -
262A GLY* 3.2 15.1 + - - -
318A PHE* 3.2 21.3 - - - -
82B GLY 2.9 11.3 + - - +
83B ASP* 3.6 6.5 - - - +
85B VAL* 1.3 75.5 - - - +
87B LEU* 1.3 59.5 + - - +
89B GLN* 3.8 1.4 - - - +
90B LYS* 2.8 71.8 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASP 2.7 22.3 + - - +
84B LYS* 3.1 14.1 + - + +
86B ASN* 1.3 71.5 - - - +
88B ARG* 1.3 64.5 + - + +
90B LYS* 3.1 19.9 + - + +
91B LEU* 3.0 44.1 + - + +
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASN* 4.2 24.9 + - - +
224A HIS* 6.1 2.9 - - - -
84B LYS* 2.9 25.2 + - + +
85B VAL* 4.2 6.3 - - - +
87B LEU* 1.3 76.0 - - + +
89B GLN* 1.3 60.1 - - - +
91B LEU* 3.4 9.9 + - - +
92B LEU* 3.1 34.1 + - + +
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 5.4 1.4 + - - -
216A VAL* 5.8 0.2 - - - +
318A PHE* 2.6 48.4 + - + -
319A PHE* 3.3 37.6 - - + +
321A VAL* 2.7 28.7 - - - +
85B VAL 3.4 9.5 + - - +
88B ARG* 1.3 76.9 - - - +
90B LYS* 1.3 58.6 + - - +
92B LEU* 2.7 27.7 + - + +
93B ASN* 2.8 40.8 + - - +
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASN* 5.6 1.2 - - - +
318A PHE* 4.3 10.5 - - + -
83B ASP 5.5 0.4 + - - -
86B ASN* 2.8 52.2 + - - +
87B LEU* 3.1 22.9 + - + +
89B GLN* 1.3 72.6 - - - +
91B LEU* 1.3 58.8 + - + +
93B ASN* 3.3 27.2 + - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.0 47.1 + - + +
88B ARG* 3.7 9.6 - - + +
90B LYS* 1.3 75.7 - - + +
92B LEU* 1.3 65.8 + - + +
93B ASN* 4.7 1.9 - - - +
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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