Contacts of the strand formed by residues 51 - 57 (chain A) in PDB entry 1E7K
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 SER 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 3.4 18.1 + - - -
46A LEU* 3.9 14.6 - - - -
49A GLY* 3.6 2.3 - - - -
50A ILE* 1.3 78.1 - - - +
52A GLU* 1.3 63.7 + - - +
53A PHE 3.5 7.1 + - - -
54A ILE* 3.2 13.2 - - - +
78A VAL* 3.6 19.1 - - - +
103A SER* 2.8 26.6 + - - -
104A VAL 3.8 3.6 - - - -
105A THR* 4.6 0.2 - - - +
106A ILE* 3.9 10.4 - - - +
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Residues in contact with GLU 52 (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 GLN* 4.7 1.0 + - - -
51A SER* 1.3 75.1 - - - +
53A PHE* 1.3 64.3 + - + +
78A VAL* 3.6 1.3 - - - +
79A PRO* 3.5 14.2 - - - +
104A VAL* 2.7 16.5 + - + +
105A THR 3.1 24.6 - - - +
106A ILE* 3.6 24.9 - - + +
107A LYS 4.7 2.3 + - - +
113A LYS* 3.8 24.0 + - - +
116A ILE* 3.4 41.4 - - + +
120A GLN* 3.1 27.9 + - - +
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Residues in contact with PHE 53 (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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22A LEU* 4.1 6.5 - - + -
25A LEU* 3.6 32.3 - - + -
26A VAL* 5.5 2.5 - - + -
51A SER* 3.5 4.5 + - - -
52A GLU* 1.3 90.4 - - + +
54A ILE* 1.3 65.6 + - - +
55A VAL* 3.6 27.8 - - + -
78A VAL* 3.5 3.6 - - - -
79A PRO* 3.0 29.6 - - + +
81A VAL* 4.9 3.4 - - + -
103A SER* 3.6 0.7 - - - -
104A VAL* 3.1 48.0 + - + -
116A ILE* 4.1 11.4 - - + -
119A ILE* 3.9 27.4 - - + -
120A GLN* 4.1 14.4 - - + -
123A ILE* 4.8 2.2 - - + -
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Residues in contact with ILE 54 (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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42A ALA* 4.4 6.7 - - + +
45A THR* 4.0 0.4 - - - +
46A LEU* 3.6 24.9 - - + -
51A SER* 3.2 10.1 - - - +
53A PHE* 1.3 75.2 - - - +
55A VAL* 1.3 71.0 + - - +
56A MET* 4.0 15.5 - - + -
69A LEU* 4.7 13.5 - - + -
73A CYS* 3.6 25.1 - - - -
78A VAL* 4.1 1.3 - - + -
79A PRO 2.9 5.7 + - - -
80A TYR* 3.2 11.9 - - + +
81A VAL* 2.9 29.1 + - - +
102A CYS 3.3 11.9 - - - +
103A SER* 3.1 33.9 - - - +
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Residues in contact with VAL 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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22A LEU* 4.4 7.4 - - + -
23A LEU* 6.1 0.2 - - + -
26A VAL* 4.4 11.7 - - + -
53A PHE* 3.6 27.8 - - + +
54A ILE* 1.3 78.1 - - - +
56A MET* 1.3 66.7 + - - +
81A VAL* 3.3 15.9 - - + +
83A VAL* 3.9 28.5 - - + -
89A LEU* 4.0 14.4 - - + +
101A ALA* 3.2 2.6 - - - +
102A CYS* 2.9 51.9 + - - +
104A VAL* 5.5 2.0 - - + -
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Residues in contact with MET 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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54A ILE* 4.0 9.6 - - + -
55A VAL* 1.3 80.8 - - - +
57A ALA* 1.3 54.5 + - - +
66A ILE* 3.9 12.1 - - + +
69A LEU* 3.6 31.0 - - + -
70A PRO* 3.9 8.7 - - + -
80A TYR* 3.7 29.4 - - + -
81A VAL 2.8 9.2 + - - +
82A PHE* 3.1 55.2 - - + -
83A VAL* 2.8 36.1 + - - +
89A LEU* 4.4 2.0 - - - -
100A ILE 3.5 9.6 - - - +
101A ALA* 4.0 10.3 - - + +
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Residues in contact with ALA 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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56A MET* 1.3 71.7 - - - +
58A ALA* 1.3 65.7 + - - +
59A ASP* 3.3 19.3 - - - +
60A ALA* 2.9 24.4 + - - +
63A LEU* 4.1 0.5 - - - +
66A ILE* 3.8 4.7 - - - +
82A PHE* 4.2 2.7 - - - -
83A VAL* 3.5 6.1 - - - -
85A SER 4.2 3.1 - - - +
86A LYS* 3.7 25.1 - - + +
89A LEU* 4.5 3.1 - - + -
99A VAL 3.8 4.3 - - - +
100A ILE* 2.8 21.0 + - - +
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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