Contacts of the strand formed by residues 82 - 90 (chain A) in PDB entry 3EER
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ALA* 3.7 38.0 - - - +
62A PHE* 4.0 19.7 - - + -
63A SER* 3.6 29.0 - - - +
66A ILE* 3.8 20.2 - - + -
80A ALA 3.3 3.8 + - - +
81A PRO* 1.3 79.3 - - - +
83A THR* 1.3 71.7 + - - +
102A LEU* 4.3 8.5 - - + -
103A ALA 3.2 10.1 - - - +
104A ALA* 4.2 4.0 - - - -
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Residues in contact with THR 83 (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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59A ALA* 5.0 0.4 - - - -
81A PRO* 4.3 0.5 - - - +
82A VAL* 1.3 75.7 + - - +
84A ALA* 1.3 66.7 + - - +
85A THR* 3.9 12.0 + - - +
101A ALA 3.7 2.4 - - - +
103A ALA* 2.9 46.2 + - + +
105A HIS* 4.8 6.9 - - - -
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Residues in contact with ALA 84 (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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55A ALA* 3.6 41.3 - - - +
58A TYR* 4.5 4.3 - - + -
59A ALA* 3.9 14.8 - - + +
82A VAL 4.0 2.6 + - - -
83A THR* 1.3 76.3 - - - +
85A THR* 1.3 62.5 + - - +
86A VAL* 4.1 4.7 - - + -
100A VAL* 5.2 0.7 - - + -
101A ALA 3.3 5.6 - - - +
102A LEU* 3.8 22.0 - - + -
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Residues in contact with THR 85 (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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83A THR* 4.4 12.3 + - - +
84A ALA* 1.3 74.3 + - - +
86A VAL* 1.3 65.5 + - - +
87A GLY 4.3 0.2 + - - -
99A SER 3.7 0.9 - - - +
100A VAL* 3.3 5.0 - - - +
101A ALA* 2.8 47.1 + - + +
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Residues in contact with VAL 86 (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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51A GLU* 3.8 39.8 - - + +
54A PHE* 4.0 23.1 - - + -
55A ALA* 3.6 33.5 - - + +
58A TYR* 5.7 0.9 - - + -
84A ALA* 4.1 3.0 + - + -
85A THR* 1.3 83.5 - - - +
87A GLY* 1.3 66.3 + - - +
98A LEU* 4.4 9.4 - - + -
99A SER 3.3 7.6 - - - +
100A VAL* 4.4 12.6 - - + -
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Residues in contact with GLY 87 (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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51A GLU* 4.6 1.1 - - - -
85A THR* 4.2 1.0 - - - +
86A VAL* 1.3 75.7 - - - +
88A ILE* 1.3 60.1 + - - -
98A LEU* 3.1 13.2 - - - +
99A SER* 2.9 45.2 + - - +
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Residues in contact with ILE 88 (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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20A ARG* 3.5 19.7 - - - +
41A MSE 4.2 22.0 - - + -
51A GLU* 3.4 39.7 - - + +
87A GLY* 1.3 76.0 - - - +
89A GLY* 1.3 62.7 + - - +
96A PHE* 4.1 31.4 - - + -
97A ALA 3.5 8.3 - - - +
98A LEU* 4.1 7.2 - - + -
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Residues in contact with GLY 89 (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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88A ILE* 1.3 77.7 - - - +
90A PRO* 1.3 75.6 - - - +
96A PHE* 3.2 10.3 - - - +
97A ALA* 2.9 33.0 + - - +
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Residues in contact with PRO 90 (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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89A GLY* 1.3 85.6 - - - +
91A ASN* 1.3 61.4 + - - +
92A GLY* 3.4 5.6 - - - +
95A GLY 3.4 11.2 - - - +
96A PHE* 3.9 13.6 - - + -
97A ALA* 4.7 0.9 - - - +
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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