Contacts of the helix formed by residues 53 - 75 (chain B) in PDB entry 2NL9
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 ARG 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PRO* 1.4 75.6 - - + +
55B GLU* 3.3 3.9 - - - +
56B ILE* 3.0 27.8 + - - +
57B TRP* 2.8 45.2 + - + +
60B GLN* 5.0 12.1 - - - +
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Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 4.0 35.9 - - + +
53B ARG* 1.4 93.6 - - + +
55B GLU* 1.3 61.7 + - + +
57B TRP* 3.2 8.3 + - + +
58B ILE* 2.9 36.1 + - + +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 2.7 34.4 + - - +
248A ARG* 2.8 48.4 + - + +
249A VAL* 3.7 22.3 - - + +
252A HIS* 6.0 0.7 - - + -
53B ARG 3.3 2.6 - - - +
54B PRO* 1.3 82.7 - - + +
56B ILE* 1.3 64.5 + - + +
58B ILE* 3.4 7.0 + - + +
59B ALA* 2.8 30.5 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS* 3.4 45.5 - - + +
1004A ZN 4.4 5.6 - - - -
53B ARG* 3.0 31.7 + - - +
55B GLU* 1.3 77.9 - - + +
57B TRP* 1.3 62.3 + - - +
59B ALA* 3.2 2.8 + - - +
60B GLN* 2.8 49.1 + - + +
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Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA* 4.6 6.3 - - - -
230A GLY* 4.1 9.4 - - - -
231A MSE 3.4 41.1 - - + -
234A LYS* 3.4 31.8 - - + +
53B ARG* 2.8 33.0 + - + +
54B PRO* 3.5 9.6 - - + +
56B ILE* 1.3 75.7 - - - +
58B ILE* 1.3 72.5 + - + +
60B GLN* 3.3 9.8 + - - +
61B GLU* 3.1 44.7 + - + +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A MSE 3.6 26.2 - - + +
234A LYS* 3.9 12.8 - - + +
235A LEU* 3.5 45.1 - - + +
249A VAL* 3.6 21.1 - - + -
270A PHE* 4.4 8.5 - - + -
54B PRO 2.9 24.5 + - - +
55B GLU* 3.7 9.9 - - + +
57B TRP* 1.3 86.4 - - + +
59B ALA* 1.3 63.5 + - - +
61B GLU* 3.1 3.8 + - - +
62B LEU* 2.9 33.0 + - + +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 3.8 13.9 - - + +
252A HIS* 3.5 31.2 - - + -
253A VAL* 3.5 24.5 - - + +
55B GLU 2.8 17.8 + - - +
56B ILE 3.7 1.8 - - - +
58B ILE* 1.3 77.6 - - - +
60B GLN* 1.3 57.2 + - - +
63B ARG* 2.8 34.0 + - - +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS* 6.1 0.2 - - - -
1003A ZN 4.6 9.9 - - - -
53B ARG* 5.0 9.8 - - - +
56B ILE* 2.8 39.2 + - + +
57B TRP* 3.3 10.4 + - + +
59B ALA* 1.3 72.4 - - - +
61B GLU* 1.3 57.0 + - - +
63B ARG* 3.4 10.0 + - - +
64B ARG* 2.9 29.5 + - - +
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Residues in contact with GLU 61 (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* 4.2 12.4 - - + +
231A MSE 3.7 22.7 - - + -
57B TRP* 3.1 30.8 + - + +
58B ILE 3.6 7.0 - - - +
60B GLN* 1.3 74.3 - - - +
62B LEU* 1.3 61.5 - - - +
64B ARG* 2.6 36.6 + - - +
65B ILE* 2.9 45.0 + - + +
1007B ZN 2.1 36.7 - - - -
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Residues in contact with LEU 62 (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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231A MSE 3.4 28.7 - - + -
246A LEU* 5.2 1.3 - - + -
249A VAL* 3.6 28.7 - - + -
253A VAL* 3.9 8.9 - - + +
263A ARG* 5.3 1.0 - - - +
266A THR* 3.8 27.8 - - + +
267A LEU* 3.6 25.4 - - + -
270A PHE* 3.8 25.4 - - + -
58B ILE* 2.9 23.7 + - + +
59B ALA 3.8 2.9 - - - +
61B GLU* 1.3 77.8 - - - +
63B ARG* 1.3 57.2 + - - +
65B ILE* 4.7 0.9 - - + -
66B GLY* 2.8 27.7 + - - -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS* 3.0 17.5 + - - -
253A VAL* 2.9 40.0 + - + +
255A SER* 3.8 4.2 + - - -
256A ASP* 3.3 34.2 + - - +
263A ARG* 3.3 32.0 + - - +
1003A ZN 3.9 20.6 - - - -
59B ALA 2.8 18.6 + - - +
60B GLN* 3.7 9.5 - - - +
62B LEU* 1.3 78.4 - - - +
64B ARG* 1.3 58.1 + - - +
67B ASP* 2.8 35.4 + - - +
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A HIS* 4.6 8.5 + - - -
227A ALA* 4.7 4.8 - - - +
60B GLN 2.9 18.1 + - - +
61B GLU* 2.6 34.6 + - - +
63B ARG* 1.3 76.0 - - - +
65B ILE* 1.3 81.2 + - - +
67B ASP* 4.0 3.2 - - - +
68B GLU* 3.0 45.3 + - + +
1007B ZN 4.1 5.9 - - - -
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A VAL* 3.7 27.8 - - + +
224A HIS* 3.7 36.8 - - + +
227A ALA* 3.9 27.8 - - + -
228A PHE* 4.1 12.3 - - + -
231A MSE 4.8 2.2 - - + -
266A THR* 3.9 9.4 - - + -
61B GLU* 2.9 28.3 + - + +
62B LEU* 4.0 3.1 - - - +
64B ARG* 1.3 88.3 - - - +
66B GLY* 1.3 59.6 + - - +
68B GLU* 3.2 8.6 + - - +
69B PHE* 2.8 28.9 + - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLY* 3.3 21.0 - - - -
263A ARG* 3.8 8.5 - - - -
266A THR* 3.3 19.4 + - - -
62B LEU 2.8 22.2 + - - -
63B ARG 3.7 0.7 - - - -
65B ILE* 1.3 73.6 - - - +
67B ASP* 1.3 58.3 + - - +
69B PHE* 3.3 0.6 + - - -
70B ASN* 2.8 26.3 + - - +
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Residues in contact with ASP 67 (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 2.0 - - - +
260A ASN* 3.0 17.3 + - - +
263A ARG* 2.7 44.9 + - - +
63B ARG* 2.8 21.6 + - - +
64B ARG* 4.1 3.1 - - - +
66B GLY* 1.3 73.0 - - - +
68B GLU* 1.3 60.7 + - - +
70B ASN* 3.4 5.0 + - - +
71B ALA* 2.9 30.1 + - - +
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Residues in contact with GLU 68 (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* 3.1 38.0 + - - -
64B ARG* 3.0 38.7 + - + +
65B ILE* 3.3 5.6 - - - +
67B ASP* 1.3 75.8 - - - +
69B PHE* 1.3 63.7 + - - +
71B ALA* 3.2 7.5 + - - +
72B TYR* 2.9 29.6 + - + +
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Residues in contact with PHE 69 (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* 3.6 28.9 - - + -
219A GLY* 4.1 6.1 - - - -
220A VAL* 3.7 33.4 - - + -
224A HIS* 5.4 2.0 - + - -
262A GLY* 4.5 1.1 - - - -
265A VAL* 3.7 27.1 - - + -
266A THR* 4.4 2.2 - - - +
318A PHE* 4.9 0.4 - - - -
319A PHE* 3.7 23.8 - + - -
65B ILE 2.8 17.1 + - - +
66B GLY 3.8 3.4 - - - +
68B GLU* 1.3 82.0 - - - +
70B ASN* 1.3 67.4 + - - +
72B TYR* 3.2 11.8 + + + +
73B TYR* 3.1 47.4 + + - -
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Residues in contact with ASN 70 (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* 3.3 37.6 - - - +
261A TRP 3.4 1.9 + - - -
262A GLY* 2.9 25.7 + - - -
318A PHE* 3.3 30.1 - - - -
66B GLY 2.8 18.8 + - - +
67B ASP* 3.6 4.9 - - - +
69B PHE* 1.3 76.1 - - - +
71B ALA* 1.3 58.6 + - - +
73B TYR 3.1 1.7 + - - -
74B ALA* 2.8 35.4 + - - +
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Residues in contact with ALA 71 (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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67B ASP 2.9 18.1 + - - +
68B GLU* 3.6 6.1 - - - +
70B ASN* 1.3 77.8 - - - +
72B TYR* 1.3 64.0 + - - +
74B ALA* 3.9 6.9 - - - +
75B ARG* 3.2 24.9 + - - +
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Residues in contact with TYR 72 (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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68B GLU* 2.9 14.3 + - + +
69B PHE* 3.4 17.9 - + + +
70B ASN 3.1 0.2 - - - -
71B ALA* 1.3 79.6 - - - +
73B TYR* 1.3 89.8 + + + +
75B ARG* 3.6 23.6 + - - +
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Residues in contact with TYR 73 (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* 4.3 5.6 + - - +
216A VAL* 3.8 17.0 - - + +
219A GLY* 6.1 0.2 - - - -
318A PHE* 3.6 36.7 - - + +
319A PHE* 3.5 43.1 - + + -
320A HIS 5.7 0.9 - - - -
321A VAL* 4.4 14.6 - - + +
69B PHE* 3.1 44.8 + + - +
72B TYR* 1.3 98.5 - + - +
74B ALA* 1.3 64.2 + - - +
75B ARG 3.2 8.9 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A PHE* 3.8 18.4 - - + -
70B ASN* 2.8 23.5 + - - +
71B ALA* 3.3 9.1 + - - +
73B TYR* 1.3 77.9 - - - +
75B ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 75 (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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71B ALA 3.2 15.6 + - - +
72B TYR* 3.6 18.6 - - - +
73B TYR 3.2 8.4 - - - +
74B ALA* 1.3 82.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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