Contacts of the helix formed by residues 57 - 68 (chain B) in PDB entry 3NC0
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 ASP 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG 4.3 0.4 + - - -
56B LEU* 1.3 70.7 - - - +
58B TYR* 1.3 61.8 + - - +
59B VAL* 3.3 13.6 + - - +
60B ASN* 3.0 37.6 + - + +
61B HIS* 3.4 15.8 + - - +
73B MET* 5.9 0.3 - - - +
94B LEU* 4.3 9.8 - - + +
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Residues in contact with TYR 58 (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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54B LYS* 6.1 2.0 - - + -
56B LEU* 3.4 42.4 + - + +
57B ASP* 1.3 71.1 - - - +
59B VAL* 1.3 66.1 + - - +
61B HIS* 3.1 5.9 + - + +
62B ALA* 3.1 25.6 + - - +
94B LEU* 3.9 23.2 - - + +
195B PRO* 3.8 7.8 - - + +
197B TYR* 3.2 55.1 - + + -
198B ASP* 2.9 40.1 + - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 3.3 9.4 + - - +
58B TYR* 1.3 81.1 - - + +
60B ASN* 1.3 63.1 + - + +
62B ALA* 3.9 1.9 + - - +
63B ARG* 3.8 15.8 + - - +
169B TYR* 4.2 7.4 + - - +
195B PRO* 3.5 26.3 - - + +
198B ASP* 6.0 2.2 - - - +
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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
----------------------------------------------------------
57B ASP* 3.0 33.4 + - + +
58B TYR 3.2 0.2 - - - -
59B VAL* 1.3 76.3 - - + +
61B HIS* 1.3 62.0 + - - +
63B ARG* 3.3 30.0 + - - +
64B ARG* 3.1 36.7 + - - +
73B MET* 3.5 30.3 - - - +
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP 3.4 5.1 + - - +
58B TYR* 3.1 14.6 + - + +
60B ASN* 1.3 75.6 - - - +
62B ALA* 1.3 67.8 + - - +
63B ARG 3.0 1.8 - - - -
64B ARG* 2.8 18.0 + - - +
65B LEU* 3.0 24.4 + - + +
70B TRP* 4.4 11.0 - + - -
94B LEU* 3.1 60.0 - - + +
95B PRO* 3.8 12.9 + - + -
101B GLN* 2.9 30.5 + - - -
197B TYR* 4.5 10.5 + + + -
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR 3.1 12.2 + - - +
59B VAL 4.2 4.5 - - - +
61B HIS* 1.3 80.0 - - - +
63B ARG* 1.3 57.6 + - - +
65B LEU* 3.6 4.7 + - - +
66B ALA* 3.0 28.8 + - - +
169B TYR* 3.7 19.4 - - + -
171B ILE* 3.7 17.5 - - + +
190B CYS* 4.0 17.5 - - + -
195B PRO* 4.3 8.7 - - + -
197B TYR* 4.6 7.7 - - + -
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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
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59B VAL 3.8 7.4 + - - +
60B ASN* 3.3 30.9 + - - +
61B HIS 3.0 0.2 - - - -
62B ALA* 1.3 77.1 - - - +
64B ARG* 1.3 81.9 + - - +
66B ALA* 3.0 2.6 + - - +
67B GLU* 2.7 63.4 + - - +
69B ASP* 3.7 26.9 + - - +
73B MET* 5.9 0.8 - - - -
169B TYR* 3.8 24.4 + - + +
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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
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60B ASN* 3.1 26.7 - - - +
61B HIS* 2.8 9.1 + - - +
63B ARG* 1.3 95.0 - - - +
65B LEU* 1.3 56.3 + - - +
68B ASP* 2.7 35.7 + - - -
69B ASP* 3.0 36.9 + - - +
70B TRP* 3.5 29.9 - - + +
71B THR* 3.9 5.9 - - - +
72B GLY* 3.2 44.6 + - - +
73B MET* 3.7 19.0 - - - +
96B LYS* 3.2 24.1 - - - +
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Residues in contact with LEU 65 (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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61B HIS* 3.0 21.4 + - + +
62B ALA* 3.6 7.0 - - - +
64B ARG* 1.3 76.4 - - - +
66B ALA* 1.3 61.3 + - - +
70B TRP* 3.7 9.1 - - + -
97B HIS 4.2 4.3 - - - +
98B TYR* 3.2 51.7 + - + -
101B GLN* 3.4 36.8 - - + +
131B LEU* 4.0 11.9 - - + -
133B VAL* 3.8 10.7 - - + +
171B ILE* 3.6 26.7 - - + -
197B TYR* 3.4 23.3 - - - +
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Residues in contact with ALA 66 (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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62B ALA 3.0 18.7 + - - +
63B ARG 3.0 3.8 + - - +
65B LEU* 1.3 76.9 - - - +
67B GLU* 1.3 61.7 + - + +
68B ASP 3.6 0.2 - - - -
98B TYR* 5.3 0.2 - - - -
133B VAL* 4.1 6.7 - - + -
135B SER* 2.7 34.6 + - - +
136B ARG* 3.7 10.6 - - - -
169B TYR* 3.5 35.7 - - + -
171B ILE* 5.3 1.6 - - + -
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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
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63B ARG* 2.7 54.1 + - + +
64B ARG 3.6 0.2 - - - -
66B ALA* 1.3 81.9 - - + +
68B ASP* 1.3 71.4 + - - +
69B ASP* 3.1 8.9 + - + +
135B SER* 5.8 0.4 - - - -
136B ARG* 3.3 41.3 + - + +
167B LYS* 5.7 5.7 + - - -
169B TYR* 5.7 6.7 - - + -
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG 2.7 12.2 + - - -
65B LEU 3.8 2.0 + - - -
66B ALA 3.6 2.2 + - - -
67B GLU* 1.3 78.4 - - - +
69B ASP* 1.3 56.3 + - - +
70B TRP* 3.0 26.6 + - - +
97B HIS* 5.4 0.5 + - - -
98B TYR* 3.2 31.3 + - - +
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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