Contacts of the helix formed by residues 58 - 73 (chain B) in PDB entry 3N2N
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 HIS 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER 4.8 2.0 + - - -
55B VAL* 2.8 12.1 + - + +
57B HIS* 1.3 97.0 + - + +
59B TRP* 1.3 64.4 + - - +
60B ASN* 3.3 2.5 - - - -
61B GLU* 3.0 36.9 - - - +
62B ILE* 3.0 25.1 + - - +
180B VAL* 4.1 17.9 - - + -
181B LYS* 3.5 56.0 - - + +
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Residues in contact with TRP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.0 21.8 - - + -
50B ASP 3.3 28.3 - - - -
51B LYS* 4.0 15.9 - - + -
55B VAL* 3.0 6.2 + - + +
56B LEU 3.9 4.3 + - - +
57B HIS 3.8 0.8 - - - -
58B HIS* 1.3 78.3 - - - +
60B ASN* 1.3 62.9 + - - +
62B ILE* 3.2 21.0 + - + -
63B TYR* 2.7 44.9 + - + +
84B VAL* 4.4 2.7 - - + -
109B LEU* 2.9 46.8 + - + -
110B GLN 4.5 5.7 + - - -
112B VAL* 3.5 40.9 + - + +
114B PRO* 3.6 25.8 - - + -
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 5.4 0.4 + - - -
57B HIS 5.3 2.8 - - - +
58B HIS* 3.3 1.0 - - - -
59B TRP* 1.3 87.1 - - - +
61B GLU* 1.3 56.1 + - - +
63B TYR* 3.9 8.2 - - - +
64B TYR* 3.0 29.1 + - - +
110B GLN 5.5 1.7 - - - +
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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
----------------------------------------------------------
57B HIS 5.8 0.2 - - - -
58B HIS* 3.0 46.6 + - - +
59B TRP 3.3 0.4 - - - -
60B ASN* 1.3 76.4 - - - +
62B ILE* 1.3 63.9 + - - +
64B TYR* 4.0 6.1 - - - +
65B PHE* 3.1 24.4 + - - +
180B VAL* 3.5 19.1 - - + +
181B LYS 4.6 0.5 + - - -
201B VAL* 3.5 31.8 - - + +
202B ASN* 5.1 5.0 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.0 14.4 - - + -
50B ASP* 3.8 22.2 - - + +
55B VAL* 4.2 15.3 - - + -
58B HIS 3.0 25.5 + - - +
59B TRP* 3.5 29.4 - - + +
61B GLU* 1.3 73.2 - - - +
63B TYR* 1.3 64.8 + - - +
65B PHE* 3.4 8.3 + - - +
66B VAL* 3.2 21.8 + - - +
148B LEU* 4.0 32.3 - - + +
180B VAL* 4.1 28.3 - - + -
201B VAL* 5.5 0.2 - - - -
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 6.2 0.4 - - - -
59B TRP* 2.7 36.8 + - + +
60B ASN* 3.9 7.4 - - - +
62B ILE* 1.3 75.3 - - - +
64B TYR* 1.3 63.2 + + + +
66B VAL* 3.1 6.0 + - - +
67B GLU* 2.6 73.0 + - + +
106B LEU* 3.2 39.3 + - + +
109B LEU* 3.8 16.6 - - + -
110B GLN* 3.6 50.4 + - + -
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Residues in contact with TYR 64 (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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60B ASN 3.0 19.8 + - - +
61B GLU* 4.0 7.2 - - - +
62B ILE 3.3 0.2 - - - -
63B TYR* 1.3 83.5 - + + +
65B PHE* 1.3 59.1 + - - +
67B GLU* 3.8 14.1 - - - -
68B GLN* 2.9 74.4 + - + +
205B PHE* 6.5 0.7 - + - -
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 4.3 2.5 - + - -
61B GLU 3.1 18.6 + - - +
62B ILE* 3.4 7.2 - - - +
64B TYR* 1.3 78.1 - - - +
66B VAL* 1.3 66.9 + - + +
69B LEU* 3.2 47.5 + - + +
146B ILE* 4.1 7.0 - - + -
148B LEU* 3.9 26.9 - - + -
178B VAL* 3.9 13.7 - - + -
201B VAL* 3.7 27.8 - - + -
204B GLY 3.9 1.8 - - - -
205B PHE* 3.4 45.2 - + + -
208B LEU* 3.8 25.1 - - + -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.8 25.8 - - + -
49B LEU* 3.6 33.7 - - + -
62B ILE* 3.4 13.2 - - + +
63B TYR* 3.1 8.6 + - - +
65B PHE* 1.3 78.6 - - + +
67B GLU* 1.3 66.7 + - - +
69B LEU* 3.3 3.3 + - - +
70B ALA* 3.0 22.2 + - - +
82B PHE* 3.6 32.5 - - + -
106B LEU* 4.0 10.1 - - + -
109B LEU* 4.0 9.4 - - + -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 2.6 59.5 + - + +
64B TYR* 3.8 15.2 - - - +
66B VAL* 1.3 72.9 - - - +
68B GLN* 1.3 75.2 + - - +
70B ALA* 3.3 2.4 + - - +
71B HIS* 2.8 62.0 + - + +
106B LEU* 3.8 15.9 - - + +
110B GLN* 4.7 3.8 + - - -
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Residues in contact with GLN 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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64B TYR* 2.9 58.9 + - + +
67B GLU* 1.3 99.3 + - - +
69B LEU* 1.3 61.0 + - - +
71B HIS* 3.9 15.8 + - - +
72B LYS* 3.0 43.2 + - - +
205B PHE* 3.5 26.5 - - + -
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Residues in contact with LEU 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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45B LEU* 5.7 0.7 - - + -
47B PHE* 3.9 21.3 - - + -
65B PHE* 3.2 48.5 + - + +
66B VAL 3.8 3.8 - - - +
68B GLN* 1.3 73.4 - - - +
70B ALA* 1.3 65.2 + - - +
72B LYS* 4.5 2.0 - - + -
73B PHE* 3.1 43.7 + - + +
78B LEU* 5.4 0.6 - - - +
80B MET* 5.3 1.2 - - - +
146B ILE* 4.2 4.7 - - + -
205B PHE* 3.8 20.6 - - + +
208B LEU* 4.7 2.7 - - + -
209B GLN* 4.1 19.1 - - + +
212B ILE* 4.0 31.4 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 5.5 0.6 - - - -
66B VAL 3.0 18.5 + - - +
67B GLU 3.5 4.5 - - - +
69B LEU* 1.3 76.8 - - - +
71B HIS* 1.3 62.1 + - + +
73B PHE 3.1 21.8 + - - +
74B ILE* 3.6 6.8 - - - +
80B MET* 4.0 31.9 - - + +
82B PHE* 5.0 0.2 - - + -
99B ARG* 5.1 1.6 + - - -
102B ILE* 4.3 6.9 - - + +
106B LEU* 3.8 24.5 - - + -
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Residues in contact with HIS 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 GLU* 2.8 52.8 + - + +
68B GLN* 4.1 18.8 + - - +
69B LEU 3.4 0.2 - - - -
70B ALA* 1.3 74.3 - - + +
72B LYS* 1.3 61.5 + - + +
74B ILE* 3.6 18.3 - - + +
106B LEU* 3.9 16.3 - - + +
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Residues in contact with LYS 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 GLN* 3.0 31.4 + - - +
69B LEU* 3.8 4.9 - - - +
70B ALA 3.2 0.2 - - - -
71B HIS* 1.3 79.7 - - + +
73B PHE* 1.3 72.7 + - + +
74B ILE* 3.8 3.5 + - - +
205B PHE* 3.4 29.6 - - + -
209B GLN* 3.4 37.1 + - + +
224B ACT 3.5 22.0 - - - +
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Residues in contact with PHE 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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69B LEU* 3.1 37.2 + - + +
70B ALA 3.1 11.1 - - - +
72B LYS* 1.3 83.3 - - + +
74B ILE* 1.3 58.7 + - - +
75B SER* 3.4 3.4 - - - +
78B LEU* 3.6 21.1 - - + +
80B MET* 4.2 0.7 - - - +
99B ARG* 2.9 19.6 + - - -
209B GLN* 3.2 43.5 - - + -
212B ILE* 3.6 26.9 - - + -
213B HIS* 3.9 13.9 - - + -
216B LEU* 3.5 23.3 - - + -
224B ACT 3.5 34.8 - - + -
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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