Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 2E9I
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 HIS 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 6.0 0.7 - - + -
47A VAL* 4.8 8.5 - - + -
48A THR 4.3 3.6 - - - -
73A PRO* 2.7 53.1 + - + -
75A GLU* 3.0 43.9 + - + +
77A GLY 3.6 10.5 + - - -
78A VAL* 1.3 79.5 - - - +
80A THR* 1.3 65.8 + - - +
81A VAL 4.3 0.2 - - - -
95A PHE 3.8 1.1 - - - +
96A GLN* 3.5 2.1 - - - -
97A PHE* 3.2 50.3 + - + +
99A VAL* 3.2 24.2 - - + +
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Residues in contact with THR 80 (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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47A VAL* 3.7 2.1 - - - +
48A THR* 2.8 51.5 + - - -
78A VAL* 4.0 8.9 + - - +
79A HIS* 1.3 78.7 + - - +
81A VAL* 1.3 59.7 + - - +
82A SER* 5.0 2.7 - - - +
94A PRO* 3.5 32.5 - - + -
95A PHE 3.3 2.7 - - - +
96A GLN* 3.4 30.6 + - + +
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Residues in contact with VAL 81 (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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31A LEU* 4.7 14.8 - - + -
45A ALA* 5.5 2.9 - - + -
46A HIS 4.0 9.6 - - - +
47A VAL* 4.2 12.3 - - + +
69A VAL* 6.3 1.8 - - + -
71A PHE* 4.2 18.6 - - + -
80A THR* 1.3 73.7 - - - +
82A SER* 1.3 63.4 + - - +
83A VAL* 3.5 26.1 + - + -
93A SER* 4.0 0.5 + - - -
94A PRO* 3.1 9.5 - - - +
95A PHE* 2.8 48.7 + - + +
97A PHE* 3.8 27.4 - - + -
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Residues in contact with SER 82 (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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44A SER* 3.2 13.0 + - - +
46A HIS* 2.9 33.4 + - - +
48A THR* 3.4 18.7 + - - -
80A THR* 4.5 1.9 + - - +
81A VAL* 1.3 73.6 + - - +
83A VAL* 1.3 62.6 + - - +
84A LYS* 3.7 10.9 + - - +
89A HIS* 4.7 13.0 - - - -
93A SER* 4.5 1.6 - - - -
94A PRO* 4.5 9.6 - - - +
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Residues in contact with VAL 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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33A LEU* 4.5 22.4 - - + -
35A ILE* 5.5 3.8 - - + -
43A MET* 5.0 14.8 - - + -
44A SER 3.5 9.0 - - - +
45A ALA* 4.7 13.5 - - + -
69A VAL* 6.1 0.2 - - + -
81A VAL* 3.5 25.8 - - + -
82A SER* 1.3 70.5 - - - +
84A LYS* 1.3 63.9 + - - +
89A HIS* 3.9 1.8 + - - -
90A VAL* 3.5 33.5 + - + +
93A SER* 3.4 22.9 + - - +
95A PHE* 4.3 14.6 - - + -
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Residues in contact with LYS 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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42A ASP 4.6 0.2 - - - +
43A MET* 3.8 2.8 - - - +
44A SER* 3.2 41.5 + - - +
82A SER* 3.7 10.2 + - - +
83A VAL* 1.3 76.5 - - - +
85A TYR* 1.3 60.2 + - - +
86A ARG 4.0 1.7 + - - -
87A GLY* 4.7 9.9 - - - +
88A GLN 3.4 15.9 - - - +
89A HIS* 3.2 55.1 + - + +
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Residues in contact with TYR 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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38A ILE* 3.4 56.4 - - + +
42A ASP* 3.9 15.1 + - + -
43A MET* 4.1 13.9 - - + -
84A LYS* 1.3 72.7 - - - +
86A ARG* 1.3 111.0 + - + +
87A GLY 3.1 0.6 + - - -
88A GLN* 2.8 32.5 + - + +
90A VAL* 4.3 16.4 - - + +
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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