Contacts of the strand formed by residues 45 - 50 (chain B) 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 PHE 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.5 14.1 - - + -
39B LEU* 3.7 20.9 - - + -
41B GLU 3.5 25.6 - - - -
42B VAL 3.1 12.4 + - - +
43B TRP 4.5 2.4 - - - +
44B PHE* 1.3 87.7 - - + +
46B GLY* 1.3 58.6 + - - +
61B LEU* 5.8 2.4 - - - +
80B PHE* 3.5 38.1 - + + -
81B ARG* 3.5 5.6 - - - +
82B ALA* 3.6 30.5 - - + -
83B LYS* 4.5 6.0 - - - +
84B PHE* 5.6 2.1 - - - -
98B THR* 4.0 16.2 - - + -
101B LEU* 4.2 25.1 - - + -
102B PHE* 4.0 19.1 - + - -
105B GLN* 5.4 0.7 - - - -
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.9 9.6 - - - -
45B PHE* 1.3 77.2 - - - +
47B LEU* 1.3 62.3 + - - -
58B TRP* 3.6 18.7 - - - -
61B LEU* 6.3 1.3 - - - -
80B PHE* 3.5 6.8 - - - -
81B ARG 2.8 32.1 + - - +
83B LYS* 4.9 3.4 - - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.6 31.0 - - + -
29B LEU* 3.8 35.2 - - + -
30B PHE* 4.0 30.8 - - + -
33B VAL* 4.5 3.1 - - + -
46B GLY* 1.3 73.5 - - - -
48B GLN* 1.3 60.0 + - - +
58B TRP* 3.5 6.4 - - - +
59B LEU* 2.9 53.0 + - + +
61B LEU* 5.6 2.5 - - + +
78B PHE* 3.9 18.2 - - + -
79B LYS 3.4 0.7 - - - -
80B PHE* 4.0 18.6 - - + -
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 1.3 74.4 - - - +
49B TYR* 1.3 67.5 + - - +
50B GLN* 5.3 1.1 - - - +
56B SER* 3.9 20.5 + - - +
57B THR 3.2 16.6 + - - +
58B TRP* 3.7 28.9 - - + -
78B PHE* 3.3 6.9 - - - +
79B LYS* 2.7 46.8 + - + +
81B ARG* 4.0 25.0 - - - +
279B ARG* 3.6 23.7 + - - -
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLN* 1.3 76.7 - - - +
50B GLN* 1.3 76.5 + - - +
51B ASP* 3.5 24.7 - - + +
55B PHE 3.3 1.2 - - - +
56B SER* 3.3 4.5 - - - -
57B THR* 2.8 71.6 + - + +
59B LEU* 3.8 43.5 - - + -
60B LYS* 5.8 0.2 + - - -
68B GLN* 3.7 19.8 + - + +
69B ASP* 3.7 14.2 + - - +
70B VAL* 3.9 20.2 - - + -
71B ARG 4.8 0.2 - - - -
77B LEU 3.9 11.4 - - - +
78B PHE* 3.7 16.6 - + + -
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLN* 5.3 1.6 - - - +
49B TYR* 1.3 80.6 - - - +
51B ASP* 1.3 64.4 + - - +
54B GLY* 3.0 29.6 + - - -
55B PHE 3.4 4.8 - - - -
56B SER* 2.6 30.5 + - - +
71B ARG* 3.2 36.5 + - + +
77B LEU 4.7 3.4 + - - -
79B LYS* 5.8 2.6 + - - +
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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