Contacts of the helix formed by residues 68 - 76 (chain C) in PDB entry 4NEF
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 ASN 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ILE* 6.2 0.9 - - + -
66C HIS* 2.9 10.6 + - - +
67C ILE* 1.4 79.9 - - - +
69C PRO* 1.4 71.6 - - - +
70C ALA* 2.9 33.0 + - - +
71C VAL* 3.0 32.8 + - + +
72C THR* 3.1 14.2 + - - -
93C GLN* 3.4 7.4 - - - -
138C THR* 5.1 0.2 - - - +
141C LEU* 4.0 10.7 - - - +
183C MET* 2.7 26.5 + - - +
184C ASN* 3.4 22.5 - - - +
185C PRO* 3.5 0.2 - - - +
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Residues in contact with PRO 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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68C ASN* 1.4 85.4 - - - +
70C ALA* 1.3 55.1 + - - +
72C THR* 3.4 2.5 + - - -
73C VAL* 3.0 34.9 + - + +
90C VAL* 3.9 20.0 - - + +
93C GLN* 3.1 22.8 - - + +
94C LEU* 4.4 14.4 - - + -
184C ASN* 3.3 17.0 - - - +
185C PRO* 3.9 11.9 - - + -
186C ALA* 3.7 27.4 - - + +
205C TRP* 5.5 4.3 - - + -
209C LEU* 4.6 3.1 - - + -
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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
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68C ASN* 2.9 14.7 + - - +
69C PRO* 1.3 78.1 - - - +
71C VAL* 1.4 56.6 + - - +
73C VAL* 3.5 0.9 + - - +
74C ALA 3.0 22.5 + - - -
138C THR* 4.1 7.0 - - + -
185C PRO* 3.9 5.6 - - + +
208C PRO* 3.7 42.6 - - + +
209C LEU* 3.9 13.0 - - + +
212C ALA* 3.1 17.5 - - + +
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Residues in contact with VAL 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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65C ALA 5.6 0.2 - - - +
66C HIS* 3.6 31.0 - - + +
68C ASN* 3.0 34.5 + - + +
70C ALA* 1.4 75.7 - - + +
72C THR* 1.4 53.8 + - - +
74C ALA* 3.3 7.6 + - + +
75C CYS* 2.9 34.8 + - - +
138C THR* 5.5 0.7 - - + -
141C LEU* 4.1 10.1 - - + -
142C VAL* 4.4 10.3 - - + -
145C ILE* 3.7 41.3 - - + -
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Residues in contact with THR 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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66C HIS* 3.2 23.8 - - - +
68C ASN 3.1 5.1 + - - -
69C PRO 3.4 7.4 + - - -
71C VAL* 1.4 74.0 - - - +
73C VAL* 1.4 61.2 + - - +
75C CYS* 3.4 3.8 + - - +
76C LEU* 3.2 19.1 + - - +
81C VAL* 5.1 5.1 - - + +
86C ALA* 3.5 43.2 - - + +
89C TYR* 3.9 13.8 - - + +
90C VAL* 3.9 9.4 - - + -
93C GLN* 2.9 24.8 + - - -
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO* 3.0 21.7 + - + +
70C ALA 3.8 4.5 - - - +
71C VAL 3.3 0.2 - - - -
72C THR* 1.4 73.3 - - + +
74C ALA* 1.3 65.0 + - - +
76C LEU* 3.1 32.5 - - + +
77C VAL* 4.6 4.2 - - - +
86C ALA* 6.5 0.2 - - + -
90C VAL* 4.8 11.2 - - + -
209C LEU* 3.8 25.1 - - + +
212C ALA* 5.5 0.2 - - + -
213C ILE* 3.8 26.6 - - + +
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Residues in contact with ALA 74 (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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70C ALA 3.0 18.3 + - - +
71C VAL* 3.3 6.0 + - - +
73C VAL* 1.3 75.8 - - - +
75C CYS* 1.4 62.0 + - - +
76C LEU 3.2 1.6 + - - -
77C VAL* 3.2 7.6 + - - +
142C VAL* 3.8 22.7 - - + -
146C PHE* 3.7 7.7 - - + -
212C ALA* 3.6 26.0 - - + +
213C ILE* 4.9 1.8 - - - +
216C SER* 2.8 28.4 + - - -
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Residues in contact with CYS 75 (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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66C HIS* 3.5 29.4 - - + -
71C VAL* 2.9 22.2 + - - +
72C THR 3.6 7.2 - - - +
73C VAL 3.3 0.2 - - - -
74C ALA* 1.4 70.8 - - - +
76C LEU* 1.3 55.3 + - - +
77C VAL 2.9 12.5 + - - -
78C GLY 3.6 0.2 + - - -
79C CYS* 2.1 68.5 + - + +
80C HIS 4.4 1.0 + - - -
81C VAL* 4.2 10.9 + - + +
145C ILE* 5.2 8.5 - - - -
146C PHE* 4.5 4.5 - - - -
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Residues in contact with LEU 76 (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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72C THR 3.2 6.2 + - - +
73C VAL* 3.1 30.6 + - + +
75C CYS* 1.3 73.9 - - - +
77C VAL* 1.4 62.0 + - + +
78C GLY 4.1 0.7 - - - -
81C VAL* 3.5 26.2 - - + +
82C SER 3.8 8.3 - - - +
83C VAL* 4.1 17.3 - - + +
86C ALA* 3.6 32.3 - - + -
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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