Contacts of the strand formed by residues 54 - 61 (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 VAL 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C VAL* 4.2 6.5 - - + +
32C VAL* 3.5 8.7 - - - +
34C VAL* 3.7 27.1 - - + -
48C ALA 3.1 22.0 - - - +
49C ALA 3.6 7.9 - - - +
51C ILE* 2.9 27.5 - - + +
52C ALA 3.7 0.8 + - - -
53C GLY* 1.3 71.3 - - - +
55C ALA* 1.3 62.2 + - - +
56C LYS 3.2 25.1 - - - +
57C VAL* 3.8 12.3 - - + -
162C PRO* 3.1 19.9 - - + +
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Residues in contact with ALA 55 (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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31C ASP* 3.7 33.4 - - + +
32C VAL 2.7 15.9 + - - +
33C THR* 5.5 0.2 - - - -
53C GLY 3.2 6.4 + - - +
54C VAL* 1.3 70.5 - - - +
56C LYS* 1.3 67.0 + - + +
162C PRO* 2.9 15.6 - - - +
163C VAL* 4.7 0.9 - - - +
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Residues in contact with LYS 56 (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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32C VAL 3.5 1.0 + - - -
33C THR* 3.2 27.1 - - + +
34C VAL 3.0 23.6 + - - -
54C VAL* 3.2 7.1 - - - +
55C ALA* 1.3 84.5 - - + +
57C VAL* 1.3 64.7 + - - +
58C LEU* 5.2 9.1 - - - +
84C TYR* 5.6 3.4 - - - +
162C PRO* 3.4 9.0 - - - -
163C VAL* 3.5 16.4 - - + -
165C GLU* 4.0 24.4 + - - +
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Residues in contact with VAL 57 (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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34C VAL* 3.3 11.4 - - + +
36C CYS* 4.9 2.0 - - - -
45C ALA* 3.9 32.1 - - + +
48C ALA* 4.1 8.5 - - + -
49C ALA* 3.6 37.5 - - + +
54C VAL* 3.8 9.9 - - + -
56C LYS* 1.3 80.9 - - - +
58C LEU* 1.3 73.3 + - - +
59C VAL* 4.6 0.4 - - + -
162C PRO* 4.2 1.3 - - + -
163C VAL 2.8 18.3 + - - +
164C THR* 3.7 6.3 - - - +
165C GLU* 2.8 33.5 + - - +
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Residues in contact with LEU 58 (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* 4.4 8.5 - - + -
33C THR* 3.9 20.0 - - - +
34C VAL 2.8 8.7 + - - +
35C LEU* 3.8 13.7 - - + -
36C CYS* 2.8 26.6 + - - -
56C LYS* 5.2 9.0 - - - +
57C VAL* 1.3 79.7 - - - +
59C VAL* 1.3 64.4 + - - +
80C LEU* 4.0 25.6 - - + -
84C TYR* 4.0 13.9 - - - +
165C GLU* 3.8 28.5 - - + +
166C THR 4.9 9.4 - - - +
167C ALA* 5.4 5.6 - - + -
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Residues in contact with VAL 59 (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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35C LEU* 4.9 1.6 - - - -
36C CYS 3.2 7.6 - - - +
41C ALA* 3.9 21.3 - - + -
42C LYS* 4.3 5.2 - - + +
45C ALA* 3.4 18.4 - - + -
57C VAL* 4.6 0.2 - - + -
58C LEU* 1.3 78.0 - - - +
60C ALA* 1.3 63.8 + - - +
61C GLU* 3.9 17.5 - - + +
164C THR* 3.3 34.5 - - + -
165C GLU 2.8 14.5 + - - +
166C THR* 3.0 32.0 - - + +
167C ALA* 3.2 6.9 + - - +
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Residues in contact with ALA 60 (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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35C LEU* 4.6 4.9 - - + -
36C CYS 2.7 9.9 + - - +
37C ALA* 3.7 20.0 - - + -
38C GLY 2.9 23.9 + - - +
41C ALA* 4.5 0.4 - - - -
59C VAL* 1.3 74.5 - - - +
61C GLU* 1.3 60.4 + - - +
62C ASP* 3.4 3.1 + - - -
65C TYR* 3.6 15.4 - - + -
76C LEU* 3.9 19.1 - - + -
166C THR* 4.5 4.3 - - - -
167C ALA* 5.1 5.2 - - + +
168C ALA 5.1 5.4 - - - +
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Residues in contact with GLU 61 (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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38C GLY 3.0 5.6 - - - +
39C ALA 3.2 23.6 - - - +
40C SER* 3.2 14.8 - - - -
41C ALA* 3.3 8.6 + - - +
42C LYS* 3.0 36.3 + - - +
59C VAL* 3.9 12.5 - - + +
60C ALA* 1.3 72.1 - - - +
62C ASP* 1.3 61.9 + - - +
166C THR* 4.8 5.0 - - + +
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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