Contacts of the helix formed by residues 58 - 73 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D SER 4.7 2.6 + - - -
55D VAL* 2.8 15.1 + - + +
57D HIS* 1.3 98.6 + + + +
59D TRP* 1.3 65.3 + - - +
60D ASN 3.3 2.7 - - - +
61D GLU* 3.3 36.0 + - - +
62D ILE* 3.2 23.5 + - - +
180D VAL* 3.5 16.2 - - + -
181D LYS* 3.4 47.5 - - + +
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Residues in contact with TRP 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 4.1 20.4 - - + -
50D ASP 3.3 29.2 - - - -
51D LYS* 3.9 16.2 - - + -
55D VAL* 3.1 5.8 + - + +
56D LEU 4.3 3.3 + - - +
57D HIS 3.8 0.4 - - - -
58D HIS* 1.3 74.2 - - - +
60D ASN* 1.3 62.4 + - - +
62D ILE* 3.1 20.3 + - + -
63D TYR* 2.7 47.7 + - + +
84D VAL* 4.4 2.2 - - + -
109D LEU* 3.0 42.0 + - + -
110D GLN* 4.9 4.3 + - - +
112D VAL* 3.5 43.7 + - + +
114D PRO* 3.7 24.2 - - + -
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Residues in contact with ASN 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D HIS 5.4 5.7 + - - +
58D HIS* 3.3 1.5 - - - -
59D TRP* 1.3 83.1 - - - +
61D GLU* 1.3 59.0 + - + +
63D TYR* 3.9 7.4 - - - +
64D TYR* 2.9 33.9 + - - +
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D HIS 5.7 0.4 - - - -
58D HIS* 3.3 28.7 + - - +
60D ASN* 1.3 73.8 - - + +
62D ILE* 1.3 65.0 + - - +
64D TYR* 4.1 4.2 - - - +
65D PHE* 3.1 24.6 + - - +
180D VAL* 3.4 15.7 - - + +
181D LYS 5.0 0.9 + - - -
201D VAL* 3.4 31.1 - - + +
202D ASN* 3.9 19.8 + - - +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 3.8 14.4 - - + -
50D ASP* 3.5 26.2 - - + +
55D VAL* 4.0 22.0 - - + -
58D HIS 3.4 14.8 - - - +
59D TRP* 3.1 28.9 + - + +
61D GLU* 1.3 76.5 - - - +
63D TYR* 1.3 65.0 + - - +
65D PHE* 3.5 3.1 + - - +
66D VAL* 3.4 21.5 + - - +
148D LEU* 3.8 28.3 - - + +
180D VAL* 3.8 28.7 - - + -
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Residues in contact with TYR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 6.1 0.4 - - - -
59D TRP* 2.7 39.7 + - + +
60D ASN* 4.0 7.0 - - - +
62D ILE* 1.3 74.7 - - - +
64D TYR* 1.3 65.8 + + + +
66D VAL* 3.1 6.9 + - - +
67D GLU* 2.8 65.5 + - + +
71D HIS* 5.6 0.2 + - - -
106D LEU* 3.3 36.7 + - + +
109D LEU* 3.7 28.5 - - + -
110D GLN* 2.8 37.1 + - + -
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Residues in contact with TYR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ASN 2.9 20.3 + - - +
61D GLU* 4.1 4.5 - - - +
62D ILE 3.3 0.2 - - - -
63D TYR* 1.3 81.5 - + + +
65D PHE* 1.3 60.1 + - - +
67D GLU* 3.4 27.1 - - - -
68D GLN* 2.9 70.4 + - + +
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Residues in contact with PHE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 4.1 2.7 - + - -
61D GLU 3.1 18.5 + - - +
62D ILE 3.5 5.2 - - - +
64D TYR* 1.3 77.0 - - - +
66D VAL* 1.3 66.7 + - + +
68D GLN* 3.6 7.7 + - - +
69D LEU* 3.2 50.8 + - + +
146D ILE* 3.9 8.3 - - + -
148D LEU* 3.7 35.7 - - + -
178D VAL* 3.9 20.6 - - + -
201D VAL* 4.4 15.9 - - + -
204D GLY* 3.5 13.2 - - - -
205D PHE* 3.4 38.3 - - + -
208D LEU* 4.2 8.3 - - + -
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 3.7 24.3 - - + -
49D LEU* 3.6 33.0 - - + -
62D ILE 3.4 13.7 - - - +
63D TYR* 3.1 9.4 + - - +
65D PHE* 1.3 78.6 - - + +
67D GLU* 1.3 60.9 + - - +
69D LEU* 3.3 3.1 + - - +
70D ALA* 2.9 28.6 + - - +
82D PHE* 3.6 33.9 - - + -
106D LEU* 3.9 11.7 - - + -
109D LEU* 4.2 6.7 - - + -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TYR* 2.8 60.7 + - + +
64D TYR* 3.4 29.7 - - - +
66D VAL* 1.3 74.1 - - - +
68D GLN* 1.3 63.4 + - - +
70D ALA* 3.4 0.3 + - - +
71D HIS* 3.1 53.1 + - + +
106D LEU* 3.9 12.3 - - + +
110D GLN* 4.4 3.6 + - - -
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Residues in contact with GLN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D TYR* 2.9 64.3 + - + +
65D PHE* 3.8 2.3 - - - +
67D GLU* 1.3 78.4 - - - +
69D LEU* 1.3 57.7 + - - +
71D HIS* 4.0 2.0 - - - +
72D LYS* 3.0 30.0 + - - +
205D PHE* 3.5 52.6 - - + +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 5.6 0.7 - - + -
47D PHE* 3.8 23.6 - - + -
65D PHE* 3.2 46.2 + - + +
66D VAL 3.3 3.3 + - - +
68D GLN* 1.3 76.3 - - - +
70D ALA* 1.3 66.2 + - - +
72D LYS* 3.2 1.8 + - - -
73D PHE* 3.0 38.8 + - + +
78D LEU* 5.4 0.7 - - - +
80D MET* 5.6 0.7 - - - -
146D ILE* 4.2 4.3 - - + -
205D PHE* 3.6 26.7 - - + +
208D LEU* 4.4 1.8 - - + -
209D GLN 4.0 16.2 - - - +
212D ILE* 3.8 31.6 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 5.3 0.8 - - - -
66D VAL* 2.9 18.6 + - + +
67D GLU 3.7 4.0 - - - +
69D LEU* 1.3 76.5 - - - +
71D HIS* 1.3 62.3 + - - +
73D PHE 3.1 23.9 - - - +
74D ILE* 4.1 3.5 - - - +
80D MET* 3.9 33.2 - - - +
82D PHE* 4.8 0.9 - - + -
99D ARG* 4.9 2.1 + - - +
102D ILE* 4.3 6.6 - - + +
106D LEU* 3.8 25.1 - - + -
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Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D GLU* 3.1 43.1 + - + +
68D GLN* 4.5 1.8 - - - +
70D ALA* 1.3 74.3 + - + +
72D LYS* 1.3 64.3 + - - +
74D ILE* 3.4 22.3 - - + +
102D ILE* 5.6 2.9 - - + +
103D ARG* 5.3 12.8 - - + -
106D LEU* 3.3 28.5 - - + +
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLN 3.0 20.4 + - - +
69D LEU* 3.2 6.7 + - - +
71D HIS* 1.3 80.8 - - - +
73D PHE* 1.3 78.6 + - + +
74D ILE* 3.8 4.4 + - - +
205D PHE* 4.7 7.4 - - + -
209D GLN* 3.4 33.7 - - + +
223D ACT 3.9 31.0 - - - +
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Residues in contact with PHE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU* 3.0 32.6 + - + +
70D ALA 3.1 11.9 - - - +
72D LYS* 1.3 89.6 - - + +
74D ILE* 1.3 57.1 + - - +
75D SER* 3.3 5.6 - - - +
78D LEU* 3.5 21.2 - - + +
80D MET* 4.2 0.2 - - - +
99D ARG* 2.9 20.4 + - - -
209D GLN* 3.2 45.1 - - + -
212D ILE* 3.7 26.5 - - + -
213D HIS* 4.0 13.2 - - + -
216D LEU* 3.6 21.1 - - + -
223D ACT 3.6 34.5 - - + -
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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