Contacts of the helix formed by residues 70 - 83 (chain C) in PDB entry 1EFP
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 ALA 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C ARG 3.3 5.7 + - - -
69C LEU* 1.3 70.1 - - - +
71C GLU* 1.3 63.5 + - - +
74C ALA* 2.9 36.6 + - - +
97C ASN* 3.6 27.3 + - - +
98C VAL* 4.4 11.0 - - - -
101C ARG* 4.1 3.8 - - - -
143D GLN* 3.5 37.2 - - + +
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Residues in contact with GLU 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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69C LEU* 2.9 5.4 + - - +
70C ALA* 1.3 78.6 + - - +
72C PRO* 1.4 72.1 - - + +
74C ALA* 4.1 1.9 - - - +
75C ALA* 3.4 15.6 + - - +
101C ARG* 3.4 25.5 + - - +
172C PRO* 4.5 14.3 - - + +
174C LEU* 3.5 35.9 - - + -
175C SER* 2.5 33.6 + - - +
142D ALA* 4.0 2.5 - - - -
143D GLN* 3.2 44.1 + - - +
170D ILE* 5.7 0.7 - - - +
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Residues in contact with PRO 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.6 50.0 - - + +
65C TYR* 4.1 8.6 + - + -
69C LEU* 2.8 34.3 - - + +
71C GLU* 1.4 86.1 - - + +
73C THR* 1.3 63.7 + - - +
75C ALA* 2.9 16.3 + - - +
76C LEU* 3.1 10.4 + - - +
170C ALA 4.4 4.5 - - - +
171C ASP* 4.4 7.4 - - - +
172C PRO* 4.3 12.3 - - + +
175C SER* 4.4 4.5 - - - +
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Residues in contact with THR 73 (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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6C LEU* 4.9 9.6 - - + -
37C ALA* 5.3 1.8 - - + -
65C TYR* 4.0 12.3 - - + -
68C ARG* 3.2 46.4 - - + +
69C LEU 3.2 9.7 + - - -
70C ALA 4.4 1.1 - - - -
72C PRO* 1.3 77.3 - - - +
74C ALA* 1.3 62.1 + - - +
76C LEU* 3.0 32.9 + - + +
77C ILE* 3.2 18.3 + - + +
98C VAL* 4.1 20.4 - - + -
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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 2.9 24.5 + - - +
71C GLU 4.1 1.6 - - - +
73C THR* 1.3 75.2 - - - +
75C ALA* 1.3 58.0 + - - +
78C VAL* 3.1 32.9 + - - +
98C VAL* 3.6 21.6 - - + +
101C ARG* 3.7 25.1 - - + +
102C VAL* 3.7 14.2 - - + +
105C LEU* 4.2 6.7 - - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLU 3.4 10.3 + - - +
72C PRO 2.9 14.1 + - - +
74C ALA* 1.3 76.7 - - - +
76C LEU* 1.3 64.4 + - - +
78C VAL* 3.5 4.4 + - - +
79C GLY* 3.0 20.8 + - - -
105C LEU* 5.1 3.3 - - - +
169C ALA 6.5 0.4 - - - -
170C ALA* 4.0 28.4 - - + +
172C PRO* 5.2 5.8 - - + -
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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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6C LEU* 6.0 0.2 - - + -
35C LEU* 4.1 18.2 - - + -
37C ALA* 3.4 33.2 - - + -
60C ALA* 3.9 12.3 - - + -
65C TYR* 3.7 32.3 + - + +
72C PRO 3.1 7.7 + - - +
73C THR* 3.0 16.8 + - + +
75C ALA* 1.3 75.4 - - - +
77C ILE* 1.3 66.1 + - + +
79C GLY* 3.0 13.2 + - - -
80C LEU* 3.4 35.2 + - + +
167C ALA* 5.0 7.4 - - + -
168C ALA 5.1 4.0 - - - +
169C ALA* 5.8 3.6 - - - +
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Residues in contact with ILE 77 (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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4C LEU* 3.8 12.7 - - + +
6C LEU* 3.9 32.1 - - + -
35C LEU* 4.2 17.5 - - + -
73C THR* 3.2 14.5 + - + +
76C LEU* 1.3 76.6 - - + +
78C VAL* 1.3 58.2 + - - +
80C LEU* 3.0 7.0 + - - +
81C ALA* 2.9 25.0 + - - +
87C ILE* 3.7 30.5 - - + -
98C VAL* 4.1 24.0 - - + -
99C MET* 4.7 8.5 - - - -
102C VAL* 4.2 18.8 - - + -
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Residues in contact with VAL 78 (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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74C ALA 3.1 20.4 + - - +
75C ALA* 3.9 4.9 - - - +
77C ILE* 1.3 75.3 - - - +
79C GLY* 1.3 63.6 + - - +
80C LEU 3.0 1.7 + - - -
81C ALA* 3.0 21.1 + - - +
82C GLY 4.3 1.9 + - - -
102C VAL* 3.8 21.3 - - + +
105C LEU* 3.7 34.1 - - + -
106C LEU* 4.1 20.2 - - + +
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Residues in contact with GLY 79 (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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75C ALA 3.0 15.1 + - - -
76C LEU 3.0 5.7 + - - -
78C VAL* 1.3 77.7 - - - +
80C LEU* 1.3 65.6 + - - +
82C GLY 4.9 1.2 + - - -
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Residues in contact with LEU 80 (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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4C LEU* 4.3 9.9 - - + -
35C LEU* 4.2 16.4 - - + -
58C LEU* 4.0 26.5 - - + -
76C LEU* 3.5 33.7 - - + +
77C ILE 3.0 7.4 + - - +
79C GLY* 1.3 80.8 - - - +
81C ALA* 1.3 59.8 + - - +
82C GLY 2.8 12.7 + - - -
83C ASP* 3.3 14.9 - - - +
84C TYR* 3.3 20.5 - - + -
167C ALA* 4.6 17.3 - - + -
168C ALA 5.8 1.1 - - - +
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Residues in contact with ALA 81 (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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4C LEU* 4.7 0.9 - - - +
77C ILE 2.9 10.0 + - - +
78C VAL* 3.0 14.9 + - - +
80C LEU* 1.3 75.3 - - - +
82C GLY* 1.3 62.3 + - - +
83C ASP 3.2 0.7 - - - -
84C TYR* 3.1 27.7 + - - +
87C ILE* 3.4 30.5 - - + -
106C LEU* 3.9 22.9 - - + -
142C LYS* 3.1 9.2 - - + -
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Residues in contact with GLY 82 (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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78C VAL 4.3 2.8 + - - -
79C GLY 4.9 1.6 + - - -
80C LEU 2.8 5.6 + - - -
81C ALA* 1.3 78.4 - - - +
83C ASP* 1.3 60.9 + - - -
84C TYR 3.4 0.7 + - - -
142C LYS* 3.8 14.1 + - - -
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Residues in contact with ASP 83 (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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2C ALA* 3.6 15.9 + - - +
80C LEU* 3.3 14.6 + - - +
81C ALA 3.2 0.8 - - - -
82C GLY* 1.3 78.3 - - - +
84C TYR* 1.3 77.1 + - + +
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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