Contacts of the strand formed by residues 74 - 81 (chain A) in PDB entry 2CWE
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 LEU 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 4.8 3.8 - - - +
70A MET* 3.2 5.5 - - - +
71A LYS* 2.7 39.8 + - - +
72A GLY 3.3 0.2 - - - -
73A ASN* 1.3 90.8 + - - +
75A VAL* 1.3 64.4 + - - +
76A GLU* 3.4 36.0 + - + +
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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
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68A THR* 4.4 15.9 - - - +
69A GLU 3.4 12.6 - - - +
70A MET* 3.5 33.6 - - + +
74A LEU* 1.3 81.8 - - - +
76A GLU* 1.3 67.0 + - - +
77A LYS* 4.3 3.7 + - + +
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Residues in contact with GLU 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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35A THR* 3.6 29.5 + - + +
36A ILE* 4.1 6.2 + - - +
37A SER* 2.6 42.6 + - - -
68A THR* 3.4 2.6 - - - -
69A GLU* 2.7 44.9 + - - +
71A LYS* 4.0 23.5 + - + +
74A LEU* 3.4 31.6 + - + +
75A VAL* 1.3 74.7 - - - +
77A LYS* 1.3 61.9 + - - +
78A TYR* 4.1 0.5 + - - -
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Residues in contact with LYS 77 (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 THR* 3.4 24.3 - - - +
36A ILE* 4.5 4.6 + - + +
51A TYR* 6.0 3.8 - - - -
55A GLU* 5.4 2.2 + - - -
58A LYS* 3.9 16.5 - - - +
65A VAL* 3.9 20.0 - - + -
67A ARG 3.7 4.3 - - - -
68A THR* 3.9 19.5 - - + +
75A VAL* 5.3 4.0 - - + +
76A GLU* 1.3 74.7 - - - +
78A TYR* 1.3 60.5 + - - +
79A TYR* 3.6 36.1 + - + +
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Residues in contact with TYR 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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32A LYS* 4.3 6.6 + - - -
33A GLU* 3.2 39.7 - - - +
34A MET* 3.5 4.5 - - - -
35A THR* 3.6 8.3 - - + -
38A GLN* 2.7 40.1 + - - -
65A VAL* 3.5 2.9 - - - -
66A LYS* 2.6 34.1 + - - +
67A ARG* 2.8 57.9 + - + +
69A GLU* 3.8 19.5 + - + -
71A LYS* 2.8 29.1 + - - -
76A GLU 4.9 0.2 - - - -
77A LYS* 1.3 73.1 - - - +
79A TYR* 1.3 56.5 + - - +
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Residues in contact with TYR 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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29A LEU* 3.8 18.7 - - + +
33A GLU* 2.8 26.7 - - - -
34A MET 2.6 23.5 + - - +
35A THR* 5.1 0.9 - - - -
36A ILE* 4.4 20.2 - - + +
39A LEU* 5.7 1.1 - - + -
51A TYR* 5.9 0.9 - - - -
54A ILE* 3.4 41.8 - - + +
55A GLU* 4.0 5.4 + - - -
58A LYS* 3.7 22.1 + - + -
63A VAL* 4.2 15.9 - - + -
64A GLU 3.3 19.7 - - - +
65A VAL* 3.7 17.5 - - + -
77A LYS* 3.6 44.7 + - + +
78A TYR* 1.3 75.3 - - - +
80A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 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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29A LEU* 4.5 4.3 - - - -
33A GLU* 4.1 7.9 - - - -
63A VAL* 3.1 7.4 - - - -
64A GLU 2.9 32.1 + - - -
66A LYS* 3.0 24.3 + - - +
79A TYR* 1.3 75.3 - - - +
81A ARG* 1.3 64.3 + - - -
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Residues in contact with ARG 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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3A LYS* 5.5 3.8 - - - +
26A LEU* 2.8 53.6 + - + +
27A LYS* 4.1 1.4 - - - +
29A LEU* 3.3 24.7 + - + +
30A ARG* 3.1 34.4 - - - +
62A LEU 3.5 9.6 - - - +
63A VAL* 4.3 1.1 - - - +
66A LYS* 3.3 11.1 + - - -
80A GLY* 1.3 74.6 - - - -
82A THR* 1.3 61.2 + - - +
83A ALA* 3.1 23.7 + - - +
84A ASP* 3.0 26.0 + - - +
85A VAL* 3.5 7.3 - - - +
86A PHE* 3.3 29.8 - - + +
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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