Contacts of the helix formed by residues 58 - 73 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C SER 5.2 0.4 + - - -
55C VAL* 2.8 12.6 + - + +
57C HIS* 1.3 96.1 + + + +
59C TRP* 1.3 65.6 + - - +
60C ASN* 3.2 6.5 - - - -
61C GLU* 3.1 32.8 + - + +
62C ILE* 3.0 24.6 + - - +
180C VAL* 4.2 25.1 - - + -
181C LYS* 3.3 41.8 + - + +
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Residues in contact with TRP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 4.0 25.6 - - + -
50C ASP 3.3 33.2 - - - -
51C LYS* 4.0 10.5 - - + -
55C VAL* 3.0 7.2 + - + +
56C LEU 4.2 3.9 + - - +
57C HIS 3.8 0.4 - - - -
58C HIS* 1.3 76.7 - - - +
60C ASN* 1.3 55.1 + - - +
62C ILE* 3.1 22.6 + - + -
63C TYR* 2.8 47.3 + - + +
84C VAL* 4.4 4.5 - - + -
109C LEU* 3.1 40.1 + - + -
110C GLN 4.5 5.9 + - - -
112C VAL* 3.5 40.7 + - + +
114C PRO* 3.5 25.8 - - + -
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Residues in contact with ASN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C HIS 3.5 21.7 + - - +
58C HIS* 3.6 2.8 - - - -
59C TRP* 1.3 76.5 + - - +
61C GLU* 1.3 70.9 + - - +
63C TYR* 4.0 6.7 - - - +
64C TYR* 3.0 32.6 + - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C HIS* 3.1 38.6 - - + +
60C ASN* 1.3 85.3 + - - +
62C ILE* 1.3 63.8 + - - +
64C TYR* 3.8 5.2 - - - +
65C PHE* 3.1 23.9 + - - +
180C VAL* 3.9 13.4 - - + +
181C LYS 5.1 0.3 + - - -
201C VAL* 3.6 38.4 - - + +
202C ASN* 4.9 3.1 - - - +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 3.9 15.5 - - + -
50C ASP* 3.6 20.4 - - + +
55C VAL* 4.2 19.5 - - + -
58C HIS 3.0 18.3 + - - +
59C TRP* 3.1 31.4 + - + +
61C GLU* 1.3 72.9 - - - +
63C TYR* 1.3 66.6 + - - +
65C PHE* 3.4 7.9 + - - +
66C VAL* 3.3 20.4 + - - +
148C LEU* 3.8 36.3 - - + +
180C VAL* 3.9 26.2 - - + -
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Residues in contact with TYR 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 6.1 0.2 - - - -
59C TRP* 2.8 37.5 + - + +
60C ASN* 4.0 5.6 - - - +
62C ILE* 1.3 74.9 - - - +
64C TYR* 1.3 65.3 + + + +
66C VAL* 3.0 7.7 + - - +
67C GLU* 2.7 68.0 + - + +
106C LEU* 3.2 43.7 + - + +
109C LEU* 3.8 24.9 - - + -
110C GLN* 3.7 34.1 - - + +
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Residues in contact with TYR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASN 3.0 19.3 + - - +
61C GLU* 3.8 6.1 - - - +
63C TYR* 1.3 83.6 - + + +
65C PHE* 1.3 58.0 + - - +
67C GLU* 3.9 9.9 - - - -
68C GLN* 2.9 78.0 + - + +
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Residues in contact with PHE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 4.4 2.2 - + - -
61C GLU 3.1 14.3 + - - +
62C ILE 3.4 9.9 - - - +
64C TYR* 1.3 77.4 - - - +
66C VAL* 1.3 66.0 + - + +
68C GLN* 4.9 0.7 - - - -
69C LEU* 3.2 46.7 + - + +
146C ILE* 4.0 7.9 - - + -
148C LEU* 3.9 34.3 - - + -
178C VAL* 4.0 12.6 - - + -
201C VAL* 3.8 21.3 - - + -
204C GLY 3.9 1.6 - - - -
205C PHE* 3.5 48.6 - + + -
208C LEU* 3.7 24.2 - - + -
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 3.7 25.0 - - + -
49C LEU* 3.6 33.4 - - + -
62C ILE* 3.3 13.7 + - + +
63C TYR* 3.0 8.1 + - - +
65C PHE* 1.3 78.6 - - + +
67C GLU* 1.3 60.7 + - - +
69C LEU* 3.3 2.4 + - - +
70C ALA* 2.9 28.4 + - - +
82C PHE* 3.6 33.2 - - + -
106C LEU* 4.1 4.5 - - + -
109C LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TYR* 2.7 59.5 + - + +
64C TYR* 3.8 14.0 - - - +
66C VAL* 1.3 74.5 - - - +
68C GLN* 1.3 76.8 + - - +
70C ALA* 3.4 1.7 + - - +
71C HIS* 2.9 61.8 + - + +
106C LEU* 3.8 15.0 - - + +
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C TYR* 2.9 61.8 + - + +
65C PHE* 4.9 0.2 - - - -
67C GLU* 1.3 102.1 + - - +
69C LEU* 1.3 59.4 + - - +
71C HIS* 3.8 11.2 + - - +
72C LYS* 3.0 39.5 + - - +
205C PHE* 3.6 25.7 - - + -
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 5.9 0.4 - - + -
47C PHE* 4.0 20.4 - - + -
65C PHE* 3.2 48.3 + - + +
66C VAL 3.8 2.9 - - - +
68C GLN* 1.3 72.5 - - - +
70C ALA* 1.3 67.9 + - - +
72C LYS* 3.3 2.3 + - + -
73C PHE* 3.1 44.2 + - + +
78C LEU* 5.6 0.4 - - - +
80C MET* 5.4 0.6 - - - +
146C ILE* 4.1 5.6 - - + -
205C PHE* 3.7 21.1 - - + +
208C LEU* 4.6 2.5 - - + -
209C GLN* 3.9 28.7 - - + +
212C ILE* 4.0 21.1 - - + -
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 5.4 1.0 - - - -
66C VAL* 2.9 18.1 + - + +
67C GLU 3.6 4.3 - - - +
69C LEU* 1.3 76.2 - - - +
71C HIS* 1.3 63.6 + - + +
73C PHE 3.2 21.7 + - - +
74C ILE* 3.9 5.5 - - - +
80C MET* 4.0 32.8 - - + +
82C PHE* 5.0 0.7 - - + -
99C ARG* 5.1 1.9 + - - +
102C ILE* 4.4 7.1 - - + +
106C LEU* 4.0 23.1 - - + -
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C GLU* 2.9 45.3 + - + +
68C GLN* 4.0 14.1 + - - +
70C ALA* 1.3 77.5 - - + +
72C LYS* 1.3 60.8 + - + +
73C PHE 3.6 0.2 + - - -
74C ILE* 3.7 17.3 - - + +
106C LEU* 3.7 22.9 - - + +
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLN* 3.0 26.9 + - + +
69C LEU* 3.3 6.5 + - + +
71C HIS* 1.3 78.1 - - - +
73C PHE* 1.3 74.0 + - + +
74C ILE* 4.0 2.1 + - - +
205C PHE* 4.7 14.6 - - + -
209C GLN* 4.1 24.1 + - - +
222C ACT 3.6 22.0 - - - +
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Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 3.1 31.9 + - + +
70C ALA 3.2 12.3 + - - +
72C LYS* 1.3 88.8 - - + +
74C ILE* 1.3 59.4 + - - +
75C SER* 3.5 3.1 - - - +
78C LEU* 3.6 19.9 - - + +
80C MET* 4.2 1.2 - - - +
99C ARG* 2.8 20.8 + - - -
209C GLN* 3.2 44.9 - - + -
212C ILE* 3.7 29.4 - - + -
213C HIS* 3.9 9.0 - - + -
216C LEU* 3.6 21.1 - - + -
222C ACT 3.6 32.5 - - + -
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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