Contacts of the strand formed by residues 72 - 80 (chain A) in PDB entry 2EE3
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 THR 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A SER* 3.2 42.4 + - - +
71A THR* 1.3 81.5 - - - +
73A TYR* 1.3 67.1 + - - +
74A THR* 5.2 0.2 - - - +
92A ARG* 4.2 35.2 - - + +
93A VAL 3.5 11.4 - - - +
94A THR* 3.4 18.3 + - - +
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Residues in contact with TYR 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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42A TYR* 4.4 4.7 - + + -
43A VAL 3.4 11.0 - - - +
44A SER* 3.7 18.6 - - - -
49A HIS* 2.9 56.3 + + - +
67A LEU* 3.9 20.4 - - + -
68A SER* 3.2 46.1 + - - -
71A THR* 3.4 27.4 - - + -
72A THR* 1.3 76.4 - - - +
74A THR* 1.3 61.1 + - - +
75A VAL* 3.2 12.5 + - + +
91A GLY 3.6 0.2 - - - +
93A VAL* 2.9 46.4 + - + +
95A THR* 4.2 9.4 - - + -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR 3.5 2.6 - - - +
42A TYR* 3.4 3.1 - - - -
43A VAL* 2.7 48.1 + - + +
45A SER* 4.3 13.7 + - - -
72A THR 4.2 0.6 - - - -
73A TYR* 1.3 68.2 - - - +
75A VAL* 1.3 64.9 + - - +
76A ARG* 4.4 21.4 - - + +
90A THR* 5.4 3.8 - - - -
91A GLY 3.9 5.4 - - - +
92A ARG* 4.5 22.2 - - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.4 1.1 - - + +
16A PHE* 3.9 16.4 - - + -
26A VAL* 3.9 17.7 - - + -
40A VAL* 3.7 24.9 - - + -
41A THR 3.8 2.7 - - - +
42A TYR* 4.2 7.9 - - + +
64A LEU* 3.5 29.6 - - + -
73A TYR* 3.7 13.9 - - + +
74A THR* 1.3 73.0 - - - +
76A ARG* 1.3 63.9 + - - +
77A VAL* 4.4 2.7 - - + -
89A LEU 3.3 2.2 - - - +
90A THR* 3.3 1.9 - - - -
91A GLY* 2.6 47.9 + - - +
93A VAL* 4.1 6.1 - - + -
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Residues in contact with ARG 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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40A VAL* 4.1 0.4 - - - -
41A THR* 2.9 47.6 + - - +
43A VAL* 6.2 3.3 - - - +
74A THR* 4.4 17.1 - - + +
75A VAL* 1.3 78.7 - - - +
77A VAL* 1.3 61.1 + - - +
78A THR* 3.1 8.3 + - - -
88A THR* 3.5 29.4 + - + +
89A LEU 3.2 3.4 - - - -
90A THR* 3.8 23.4 - - + +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.2 7.0 - - + -
26A VAL* 4.0 13.5 - - + -
28A TRP* 3.7 40.6 - - + -
38A VAL* 3.5 28.5 - - + -
40A VAL* 3.7 26.0 - - + -
75A VAL* 4.4 1.8 - - + -
76A ARG* 1.3 67.8 - - - +
78A THR* 1.3 58.2 + - - +
79A CYS* 3.6 15.3 + - - -
87A SER 3.8 0.3 - - - +
88A THR* 3.5 2.2 - - - -
89A LEU* 3.0 38.0 + - + +
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Residues in contact with THR 78 (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 VAL* 3.4 1.8 - - - -
39A ARG* 2.7 49.8 + - - -
41A THR* 4.1 7.4 + - - +
76A ARG 3.1 10.1 + - - -
77A VAL* 1.3 71.1 - - - +
79A CYS* 1.3 58.5 + - - +
80A LEU* 3.6 23.5 + - + +
86A SER* 4.7 9.4 - - - +
87A SER 3.3 15.5 - - - +
88A THR* 3.8 18.2 - - - +
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Residues in contact with CYS 79 (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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28A TRP* 5.2 8.5 - - - -
31A ALA* 5.0 12.8 - - - -
35A VAL* 4.1 13.7 - - + -
37A LEU 3.7 5.4 - - - -
38A VAL* 4.1 10.1 - - + -
77A VAL* 4.0 24.9 - - - -
78A THR* 1.3 72.0 - - - +
80A LEU* 1.3 60.3 + - - +
81A TYR* 3.1 38.6 + - + +
86A SER* 3.6 2.6 - - - -
87A SER* 3.1 24.2 + - - +
89A LEU* 5.5 7.2 - - - -
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Residues in contact with LEU 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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35A VAL* 3.2 14.5 - - - +
36A ARG* 3.4 23.8 - - - +
37A LEU* 3.0 23.6 + - + +
39A ARG* 4.3 19.5 - - + +
78A THR* 3.6 27.6 + - + +
79A CYS* 1.3 68.2 - - - +
81A TYR* 1.3 67.3 + - - +
85A GLY 5.0 1.1 - - - +
86A SER* 3.7 21.1 - - - +
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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