Contacts of the helix formed by residues 65 - 77 (chain A) in PDB entry 1E0C
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 PRO 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLN 5.4 0.2 - - - +
54A LEU* 3.8 27.8 - - + +
63A GLN 3.8 0.2 - - - -
64A PRO* 1.3 95.4 - - + +
66A ARG* 1.3 65.5 + - - +
67A GLU* 4.4 3.4 - - + +
68A GLN* 3.2 30.8 + - + +
69A LEU* 3.2 16.7 + - - +
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Residues in contact with ARG 66 (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 PRO 3.8 0.2 + - - -
65A PRO* 1.3 71.5 - - - +
67A GLU* 1.3 59.0 + - - +
69A LEU* 3.1 5.1 + - - +
70A GLU* 2.8 66.7 + - + +
141A LEU* 2.8 28.9 + - - +
143A LEU* 3.7 45.5 - - + +
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Residues in contact with GLU 67 (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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65A PRO* 3.3 2.5 + - + +
66A ARG* 1.3 81.0 - - - +
68A GLN* 1.3 81.5 + - - +
70A GLU* 3.4 6.8 + - - +
71A SER* 3.0 38.2 + - - +
138A PRO* 5.6 0.2 - - - +
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Residues in contact with GLN 68 (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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51A ARG* 5.0 4.0 + - - +
64A PRO* 4.1 15.7 - - + -
65A PRO* 3.2 36.9 + - + +
67A GLU* 1.3 99.6 + - - +
69A LEU* 1.3 58.1 + - - +
71A SER* 3.8 5.3 - - - -
72A LEU* 2.9 30.8 + - - +
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Residues in contact with LEU 69 (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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63A GLN* 4.6 10.8 - - + +
64A PRO* 3.6 46.0 - - + +
65A PRO 3.2 9.4 + - - +
66A ARG* 3.1 7.5 + - - +
68A GLN* 1.3 73.9 - - - +
70A GLU* 1.3 61.6 + - - +
72A LEU* 4.2 8.3 - - + -
73A PHE* 2.8 53.5 + - + +
101A LEU* 4.4 15.7 - - + -
104A VAL* 5.0 1.6 - - + -
105A ILE* 4.7 5.6 - - + -
141A LEU* 3.6 12.6 - - + -
143A LEU* 4.1 28.7 - - + -
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Residues in contact with GLU 70 (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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66A ARG* 2.8 60.4 + - + +
67A GLU* 3.9 6.5 - - - +
69A LEU* 1.3 73.7 - - - +
71A SER* 1.3 60.5 + - - +
74A GLY 3.0 17.3 + - - -
138A PRO* 3.2 13.4 - - + +
139A VAL* 3.1 36.1 + - - +
140A ALA* 3.5 7.5 - - - +
141A LEU* 2.9 34.5 + - + -
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Residues in contact with SER 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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51A ARG* 5.3 2.0 - - - -
67A GLU* 3.0 23.4 + - - +
68A GLN* 3.8 4.9 - - - -
70A GLU* 1.3 74.6 - - - +
72A LEU* 1.3 66.6 + - - +
74A GLY* 3.2 1.6 + - - -
75A GLU* 2.9 40.3 + - - +
136A GLY 5.0 0.7 - - - +
138A PRO* 4.0 19.6 - - - +
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Residues in contact with LEU 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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47A VAL* 3.9 39.0 - - + -
51A ARG* 3.6 52.0 - - + +
52A THR* 5.6 0.2 - - + -
68A GLN 2.9 19.2 + - - +
69A LEU* 3.7 12.6 - - + +
71A SER* 1.3 78.0 - - - +
73A PHE* 1.3 74.5 + - + +
75A GLU* 3.1 5.7 + - - +
76A LEU* 3.0 38.0 + - + +
98A PHE* 4.5 8.1 - - + -
101A LEU* 5.4 4.3 - - + -
375A EDO 3.9 4.9 - - - -
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Residues in contact with PHE 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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69A LEU* 2.8 46.0 + - + +
72A LEU* 1.3 79.3 - - + +
74A GLY* 1.3 62.8 + - - +
76A LEU* 3.3 8.5 + - + +
77A GLY 3.1 4.7 + - - -
78A HIS* 2.9 38.8 + - + +
84A TYR* 3.3 21.5 - + - -
98A PHE* 3.7 29.8 - + - -
101A LEU* 4.8 10.5 - - + -
102A LEU* 3.6 20.2 - - + -
105A ILE* 3.5 40.6 - - + -
139A VAL* 4.0 10.8 - - + -
141A LEU* 4.2 9.4 - - + -
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Residues in contact with GLY 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 GLU 3.0 15.0 + - - -
71A SER 3.7 2.5 - - - -
73A PHE* 1.3 75.9 - - - +
75A GLU* 1.3 63.2 + - - +
77A GLY* 3.1 9.6 + - - -
78A HIS 4.8 0.4 - - - -
135A ALA* 3.4 2.3 - - - +
136A GLY 3.2 24.7 + - - -
137A GLY 3.2 22.6 - - - +
139A VAL* 3.9 12.4 - - - +
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Residues in contact with GLU 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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45A ARG* 4.2 2.3 + - - -
51A ARG* 2.8 22.2 + - - -
71A SER* 2.9 29.5 + - - +
72A LEU* 3.1 5.3 + - - +
74A GLY* 1.3 77.7 - - - +
76A LEU* 1.3 57.5 + - - +
134A PRO* 3.3 21.0 - - + +
135A ALA 3.0 20.8 + - - -
136A GLY 3.7 10.5 + - - +
375A EDO 2.4 42.6 + - - +
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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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26A ILE* 3.6 25.0 - - + +
28A VAL* 4.4 8.1 - - + -
45A ARG* 3.7 44.6 + - + +
47A VAL* 3.9 17.7 - - + -
72A LEU* 3.0 22.9 + - + +
73A PHE* 3.7 19.1 - - + +
74A GLY 3.2 0.2 - - - -
75A GLU* 1.3 76.3 - - - +
77A GLY* 1.3 60.1 + - - +
78A HIS 4.6 1.8 - - - +
79A ARG* 4.5 1.4 + - - -
84A TYR* 4.3 8.5 - - + -
98A PHE* 3.7 31.2 - - + -
135A ALA* 4.3 1.1 - - - -
375A EDO 3.8 19.1 - - - -
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Residues in contact with GLY 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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26A ILE* 3.5 2.8 - - - +
73A PHE 3.1 2.6 + - - -
74A GLY 3.1 7.2 + - - -
75A GLU 3.2 0.6 - - - -
76A LEU* 1.3 79.4 - - - +
78A HIS* 1.3 69.6 + - - +
79A ARG* 2.8 33.7 + - - +
135A ALA* 3.0 27.4 - - - -
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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