Contacts of the helix formed by residues 70 - 83 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ARG 3.3 5.6 + - - -
69A LEU* 1.3 70.5 - - - +
71A GLU* 1.3 73.0 + - - +
74A ALA* 3.0 32.1 + - - +
97A ASN* 3.4 31.8 + - - +
98A VAL* 4.6 9.9 - - - -
101A ARG* 3.5 3.9 - - - -
143B GLN* 3.5 24.9 - - + +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU 3.1 0.2 + - - -
70A ALA* 1.3 76.8 + - - +
72A PRO* 1.3 73.9 - - + +
74A ALA* 4.2 1.4 - - - +
75A ALA* 3.3 19.1 + - - +
101A ARG* 3.8 26.5 + - - +
172A PRO* 3.7 23.9 - - + +
174A LEU* 4.1 19.3 - - + -
175A SER* 2.6 32.0 + - - +
142B ALA* 4.0 16.9 - - - +
143B GLN* 3.3 36.6 + - - +
170B ILE* 6.1 0.2 - - - +
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Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.7 48.7 - - + +
65A TYR* 3.9 9.1 + - + -
69A LEU* 3.0 34.5 - - + +
71A GLU* 1.3 86.0 - - + +
73A THR* 1.3 66.1 + - - +
75A ALA* 2.9 15.4 + - - +
76A LEU 3.1 9.4 + - - -
170A ALA 4.2 10.8 - - - +
171A ASP* 4.2 8.7 - - - +
172A PRO* 4.2 5.8 - - + +
175A SER* 4.5 5.4 - - - +
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.0 9.0 - - + -
37A ALA* 5.2 6.5 - - + -
65A TYR* 4.0 19.5 - - + -
68A ARG* 3.2 40.7 - - + +
69A LEU 3.1 16.9 + - - -
72A PRO* 1.3 77.6 - - - +
74A ALA* 1.3 58.2 + - - +
76A LEU* 2.9 27.2 + - + +
77A ILE* 3.1 17.6 + - + +
98A VAL* 4.1 20.0 - - + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 3.0 23.6 + - - +
71A GLU 4.2 1.6 - - - +
73A THR* 1.3 75.1 - - - +
75A ALA* 1.3 60.0 + - - +
77A ILE 3.7 0.3 + - - -
78A VAL* 3.2 30.1 + - - +
98A VAL* 3.6 9.7 - - + +
101A ARG* 3.8 23.8 - - + +
102A VAL* 3.6 25.0 - - + +
105A LEU* 4.2 7.6 - - + -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU 3.3 11.8 + - - +
72A PRO* 2.9 13.6 + - + +
74A ALA* 1.3 78.1 - - - +
76A LEU* 1.3 65.3 + - - +
78A VAL* 4.0 4.8 - - - +
79A GLY* 3.1 17.7 + - - -
105A LEU* 5.2 2.7 - - - +
170A ALA* 4.3 27.4 - - + +
172A PRO* 4.8 7.0 - - + -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.2 11.9 - - + -
37A ALA* 3.5 32.3 - - + -
60A ALA* 3.7 12.8 - - + -
65A TYR* 3.4 34.7 + - + +
72A PRO 3.1 4.8 + - - -
73A THR* 2.9 13.1 + - + +
75A ALA* 1.3 76.0 - - - +
77A ILE* 1.3 66.0 + - + +
79A GLY* 3.0 12.5 + - - -
80A LEU* 3.3 45.1 - - + +
167A ALA* 4.5 13.9 - - + -
168A ALA 5.3 4.0 - - - +
169A ALA* 5.6 4.0 - - - +
170A ALA* 5.7 0.2 - - - +
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.1 12.0 - - + +
6A LEU* 4.0 28.3 - - + -
35A LEU* 4.4 16.8 - - + -
73A THR* 3.1 12.2 + - + +
76A LEU* 1.3 76.8 - - + +
78A VAL* 1.3 58.5 + - - +
80A LEU* 3.0 7.1 + - - +
81A ALA* 2.8 24.6 + - - +
87A ILE* 3.8 31.0 - - + -
98A VAL* 3.9 26.9 - - + -
99A MET* 4.7 9.0 - - - -
102A VAL* 4.0 22.4 - - + -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA 3.2 18.0 + - - +
75A ALA* 4.0 4.9 - - - +
77A ILE* 1.3 75.8 - - - +
79A GLY* 1.3 64.6 + - - +
80A LEU 3.0 1.6 + - - -
81A ALA* 3.1 19.4 + - - +
82A GLY 4.3 2.6 + - - -
102A VAL* 3.9 20.9 - - + +
105A LEU* 3.8 34.3 - - + +
106A LEU* 3.7 20.8 - - + +
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ALA 3.1 10.8 + - - -
76A LEU 3.0 9.2 + - - -
78A VAL* 1.3 77.9 - - - +
80A LEU* 1.3 65.5 + - - +
82A GLY 5.0 1.5 + - - -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.3 10.5 - - + -
35A LEU* 3.8 22.0 - - + -
58A LEU* 4.3 20.6 - - + -
76A LEU* 3.3 38.8 - - + +
77A ILE 3.0 7.3 + - - +
79A GLY* 1.3 84.3 - - - +
81A ALA* 1.3 57.5 + - - +
82A GLY* 2.9 13.0 + - - -
83A ASP* 3.4 10.7 + - - +
84A TYR* 3.3 22.1 - - + -
167A ALA* 4.9 12.1 - - + -
168A ALA 6.1 0.4 - - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 5.1 1.1 - - - -
77A ILE* 2.8 11.7 + - + +
78A VAL* 3.1 17.6 + - - +
80A LEU* 1.3 75.6 - - - +
82A GLY* 1.3 63.3 + - - +
83A ASP 3.2 0.4 - - - -
84A TYR* 2.9 30.1 + - - +
87A ILE* 3.4 29.8 - - + -
106A LEU* 4.1 18.6 - - + -
142A LYS* 3.2 7.1 + - - -
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL 4.3 2.8 + - - -
79A GLY 5.0 1.6 + - - -
80A LEU 2.9 5.4 + - - -
81A ALA* 1.3 77.3 - - - +
83A ASP* 1.3 61.7 + - - +
84A TYR 3.8 0.2 + - - -
142A LYS* 3.9 14.6 + - - -
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 4.0 11.8 + - - +
80A LEU* 3.4 10.9 + - - +
81A ALA 3.2 0.6 - - - -
82A GLY* 1.3 78.9 - - - +
84A TYR* 1.3 79.2 + - + +
85A SER 4.4 0.2 + - - -
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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