Contacts of the strand formed by residues 54 - 61 (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 VAL 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.1 7.4 - - + +
32A VAL* 3.6 9.4 - - - +
34A VAL* 3.7 27.1 - - + -
48A ALA 3.2 21.8 - - - +
49A ALA* 3.4 14.1 - - - +
51A ILE* 2.9 22.9 + - + +
52A ALA 3.7 0.2 - - - -
53A GLY* 1.3 75.4 - - - +
55A ALA* 1.3 57.0 + - - +
56A LYS 3.2 27.1 - - - +
57A VAL* 4.0 8.1 - - + -
160A THR* 4.6 4.2 + - - -
162A PRO* 3.0 19.6 - - + +
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Residues in contact with ALA 55 (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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31A ASP* 3.7 32.8 - - + +
32A VAL 2.6 17.6 + - - +
33A THR* 5.5 0.2 - - - -
53A GLY 3.2 5.9 + - - +
54A VAL* 1.3 71.8 - - - +
56A LYS* 1.3 67.8 + - + +
160A THR* 5.9 0.4 - - - -
162A PRO* 2.9 15.2 - - - +
163A VAL 4.6 0.2 + - - -
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Residues in contact with LYS 56 (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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32A VAL 3.5 0.4 + - - -
33A THR* 3.2 27.5 - - + -
34A VAL 3.0 22.7 + - - -
54A VAL* 3.2 9.0 - - - +
55A ALA* 1.3 84.9 - - + +
57A VAL* 1.3 65.6 + - - +
58A LEU* 5.2 10.5 - - - +
84A TYR* 5.6 4.0 - - - +
162A PRO* 3.6 9.4 - - - -
163A VAL* 3.4 26.3 - - + +
165A GLU* 3.5 20.2 + - - -
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Residues in contact with VAL 57 (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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34A VAL* 3.4 7.9 - - + +
36A CYS* 4.8 2.0 - - - -
45A ALA* 3.6 37.0 - - + +
48A ALA* 3.9 10.5 - - + -
49A ALA* 3.6 38.8 - - + +
54A VAL* 4.0 7.9 - - + -
56A LYS* 1.3 79.6 - - - +
58A LEU* 1.3 75.0 + - - +
59A VAL* 4.3 1.8 - - + -
162A PRO* 4.5 0.4 - - + -
163A VAL* 2.9 18.0 + - - +
164A THR* 3.3 5.8 + - + -
165A GLU 3.0 23.6 + - - -
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Residues in contact with LEU 58 (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* 4.5 8.1 - - + -
33A THR* 4.1 11.9 - - - +
34A VAL 2.8 8.5 + - - +
35A LEU* 3.9 13.5 - - + -
36A CYS* 2.8 28.1 + - - +
56A LYS* 5.2 8.5 - - - -
57A VAL* 1.3 75.3 - - - +
59A VAL* 1.3 66.2 + - - +
80A LEU* 4.3 23.1 - - + -
84A TYR* 3.9 21.8 - - - +
165A GLU* 4.0 33.4 - - + +
166A THR 4.9 6.3 - - - +
167A ALA* 5.5 6.3 - - + -
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Residues in contact with VAL 59 (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* 4.7 1.3 - - - -
36A CYS 3.2 2.5 - - - +
41A ALA* 3.8 33.0 - - + +
42A LYS* 4.1 6.5 - - + +
45A ALA* 3.3 27.8 - - + -
58A LEU* 1.3 78.7 - - - +
60A ALA* 1.3 64.2 + - - +
61A GLU* 3.8 10.8 - - + +
164A THR* 3.5 15.9 - - + -
165A GLU 3.3 20.6 + - - +
166A THR* 3.3 10.8 - - + +
167A ALA* 2.9 24.9 + - - -
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Residues in contact with ALA 60 (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* 4.4 5.2 - - + -
36A CYS 2.7 9.1 + - - +
37A ALA* 3.8 6.5 - - + -
38A GLY 2.8 26.0 + - - +
41A ALA* 4.4 0.2 - - - -
59A VAL* 1.3 74.0 - - - +
61A GLU* 1.3 60.2 + - - +
62A ASP* 3.5 1.8 + - - -
65A TYR* 3.6 15.4 - - + -
76A LEU* 3.7 30.3 - - + -
166A THR* 5.5 0.4 - - - -
167A ALA* 4.5 14.4 - - + +
168A ALA 5.0 3.4 - - - +
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Residues in contact with GLU 61 (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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38A GLY 3.0 5.4 - - - -
39A ALA 3.2 24.0 - - - +
40A SER* 3.4 3.3 - - - -
41A ALA* 2.9 10.3 + - - +
42A LYS* 2.9 47.9 + - - +
59A VAL* 3.8 10.6 - - + +
60A ALA* 1.3 72.5 - - - +
62A ASP* 1.3 65.8 + - - +
166A THR* 5.6 3.2 - - - +
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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