Contacts of the strand formed by residues 70 - 76 (chain A) in PDB entry 6EKK
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 ASN 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLY 5.0 0.3 - - - -
69A GLN* 1.3 94.7 + - - +
71A PHE* 1.3 66.7 + - - +
87A CYS 3.1 15.9 + - - +
88A ARG* 3.6 22.4 - - - +
110A TYR* 3.8 40.9 + - + +
113A LEU* 5.0 0.2 - - - +
114A ASN* 5.2 3.2 + - - +
170A ARG* 3.2 26.8 + - - +
203A LYS* 5.6 0.2 - - - +
204A LEU* 4.8 0.2 - - - +
205A SER* 3.0 29.6 + - - -
404A EDO 4.8 1.8 - - - -
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Residues in contact with PHE 71 (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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53A PHE 3.6 19.5 - - - -
54A CYS 3.6 19.3 - - - -
56A PRO* 3.9 15.9 - - + -
68A GLY 6.3 0.4 - - - -
69A GLN 4.3 4.9 - - - -
70A ASN* 1.3 79.8 - - - +
72A THR* 1.3 62.5 + - - +
73A PHE* 4.1 7.9 - + - -
87A CYS* 2.7 65.5 + - + +
89A LEU* 3.9 20.4 - - + -
96A CYS* 4.7 0.2 - - - -
110A TYR* 3.5 7.1 + - - -
204A LEU* 3.5 47.6 - - + +
208A THR* 3.8 6.1 - - + +
230A VAL* 4.2 15.7 - - + -
404A EDO 3.9 1.8 - - - -
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Residues in contact with THR 72 (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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71A PHE* 1.3 78.2 + - - +
73A PHE* 1.3 69.7 + - - +
84A PHE* 3.9 11.4 - - + -
85A GLY 3.2 6.7 - - - +
86A PHE* 3.3 31.8 - - + -
106A PHE* 3.4 28.0 - - + -
110A TYR* 2.7 23.4 + - - -
208A THR* 3.3 21.7 + - - +
212A HIS* 3.2 21.6 + - - +
229A PRO* 3.8 1.7 - - - +
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Residues in contact with PHE 73 (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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50A LEU* 3.5 30.5 - - + -
53A PHE* 3.5 50.9 - - + -
54A CYS* 4.2 2.2 - - - -
71A PHE* 4.1 3.0 - + - -
72A THR* 1.3 76.8 - - - +
74A VAL* 1.3 66.2 + - - +
75A LEU* 3.8 30.3 - - + -
84A PHE* 3.5 1.2 - - - -
85A GLY* 2.7 54.6 + - - -
87A CYS* 3.5 26.0 - - - -
98A CYS* 3.8 5.6 - - - -
100A LEU* 4.3 0.7 - - + -
229A PRO* 4.6 2.0 - - - -
230A VAL* 3.5 28.3 - - + +
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Residues in contact with VAL 74 (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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53A PHE* 4.6 6.6 - - - -
73A PHE* 1.3 82.2 - - - +
75A LEU* 1.3 84.6 + - - +
76A THR* 4.2 7.1 + - - +
82A GLN* 3.8 25.8 - - + -
83A ARG 3.2 5.4 - - - +
84A PHE* 3.5 30.1 - - + -
212A HIS* 3.5 20.4 - - + -
227A TYR* 4.4 13.6 - - + +
228A ILE* 5.1 3.1 - - - +
229A PRO* 3.7 23.1 - - + +
230A VAL 5.6 0.4 + - - +
40C THR 4.2 2.3 - - - +
41C ILE* 5.0 4.3 - - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 5.1 2.9 - - + -
49A THR* 4.8 12.8 - - - -
50A LEU* 4.3 11.4 - - + -
53A PHE* 3.9 31.9 - - + -
73A PHE* 3.8 26.5 - - + -
74A VAL* 1.3 82.5 - - - +
76A THR* 1.3 61.3 + - - +
82A GLN* 3.6 0.2 - - - -
83A ARG* 2.8 67.9 + - + +
100A LEU* 4.2 13.7 - - + -
40C THR* 3.2 19.7 - - + +
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Residues in contact with THR 76 (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 ARG* 4.0 10.3 + - - +
74A VAL* 4.1 7.2 + - - +
75A LEU* 1.3 74.5 - - - +
77A ASP* 1.3 64.2 + - - +
80A SER* 3.5 37.7 - - - +
81A LYS 3.5 3.8 - - - +
82A GLN* 4.7 3.2 - - + +
83A ARG* 3.8 1.6 - - - -
227A TYR* 4.0 14.0 + - - +
38C ILE 3.5 1.2 - - - +
39C THR* 3.0 27.9 - - - -
40C THR 3.0 6.7 + - - -
41C ILE* 3.7 8.2 + - - -
42C GLY* 3.6 29.2 - - - -
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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