Contacts of the strand formed by residues 76 - 82 (chain A) in PDB entry 1EF1
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 LEU 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.1 21.3 - - + -
6A SER 2.9 15.7 + - - +
7A VAL* 3.5 9.0 - - + +
8A ARG* 2.8 26.9 + - - +
65A VAL* 3.8 29.4 - - + -
66A THR* 5.9 2.5 - - + +
70A VAL* 4.2 25.6 - - + -
71A ARG 3.9 17.7 - - - +
72A LYS* 4.9 2.0 - - - -
73A GLU* 3.5 21.5 + - - +
75A PRO* 1.3 71.0 - - - +
77A LEU* 1.3 60.4 + - - +
78A PHE* 3.8 15.7 - - + -
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Residues in contact with LEU 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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8A ARG* 3.6 50.3 - - + +
49A TYR* 3.8 19.9 - - - +
50A GLN 4.7 1.9 + - - -
73A GLU* 3.7 25.2 + - - +
75A PRO* 3.5 13.2 + - + +
76A LEU* 1.3 72.5 - - - +
78A PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 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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7A VAL* 3.6 28.7 - - + -
8A ARG 2.9 9.9 + - - +
9A VAL* 3.3 12.0 - - + -
10A THR* 3.0 26.2 + - - -
29A LEU* 3.7 20.9 - - + -
47A LEU* 4.1 18.4 - - + -
48A GLN 3.3 9.6 - - - +
49A TYR* 3.6 27.4 - + + -
59A LEU* 3.3 27.6 - - + -
65A VAL* 3.7 24.2 - - + -
70A VAL* 4.1 9.4 - - + -
76A LEU* 3.8 16.8 - - + -
77A LEU* 1.3 74.6 - - - +
79A LYS* 1.3 64.7 + - - +
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Residues in contact with LYS 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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10A THR* 3.4 15.9 - - + +
47A LEU* 3.5 3.8 - - - -
48A GLN* 2.7 49.9 + - + +
50A GLN* 5.7 2.6 + - - -
78A PHE* 1.3 76.3 - - - +
80A PHE* 1.3 61.4 + - - +
81A ARG* 3.5 26.9 + - + +
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Residues in contact with PHE 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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9A VAL* 4.0 8.9 - - + +
10A THR 2.8 14.6 + - - +
11A THR* 3.9 28.4 - - + -
12A MSE 4.4 4.5 + - - +
30A PHE* 3.7 25.6 - + - -
33A VAL* 3.8 16.4 - - + -
34A VAL* 3.9 11.9 - - + -
37A ILE* 4.0 6.1 - - + -
39A LEU* 3.4 26.2 - - + -
45A PHE* 3.3 38.3 - + + -
46A GLY 3.5 9.9 - - - -
47A LEU* 3.8 17.2 - - + +
78A PHE 4.0 0.8 + - - -
79A LYS* 1.3 70.8 - - - +
81A ARG* 1.3 63.9 + - - +
101A LEU* 3.8 19.7 - - + -
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Residues in contact with ARG 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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12A MSE 3.9 19.0 - - - -
45A PHE* 3.5 9.6 - - - -
46A GLY* 2.9 32.4 + - - +
48A GLN* 4.0 22.6 - - - +
58A TRP* 3.9 16.3 - - + -
79A LYS* 3.5 25.9 + - + +
80A PHE* 1.3 80.8 - - - +
82A ALA* 1.3 62.8 + - - +
105A GLN* 3.6 35.6 + - - +
108A GLU* 3.0 26.7 + - - -
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Residues in contact with ALA 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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44A PHE 3.4 6.1 - - - +
45A PHE* 3.6 17.7 - - + -
58A TRP* 3.9 7.4 - - - -
81A ARG* 1.3 71.4 - - - +
83A LYS* 1.3 60.4 + - - +
84A PHE 3.7 4.5 - - - +
85A TYR* 4.5 4.7 - - + -
102A PHE* 3.6 40.4 - - + -
105A GLN* 2.9 34.9 + - - +
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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