Contacts of the strand formed by residues 73 - 81 (chain A) in PDB entry 7EHI
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 SER 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLY 5.1 0.9 + - - -
29A ARG* 3.5 33.4 + - - +
30A THR 3.1 14.5 + - - -
31A ALA* 5.1 0.7 - - - -
32A LYS 3.7 1.3 - - - +
69A SER* 3.1 7.1 + - - -
70A ASP* 2.8 36.0 + - - -
72A ILE* 1.3 86.4 + - - +
74A ASP* 1.3 64.0 + - - +
75A PHE* 3.8 10.6 - - - -
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Residues in contact with ASP 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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28A LEU 3.8 0.3 - - - +
29A ARG* 3.4 5.0 - - - +
30A THR* 2.8 44.7 + - - +
31A ALA 3.9 1.6 - - - +
32A LYS* 3.6 8.9 + - - +
33A ASP* 2.8 29.0 + - - +
34A ASP 4.7 0.2 + - - -
35A ILE 4.9 2.3 - - - +
66A LYS* 2.9 34.8 + - + +
68A MET 3.6 3.1 - - - -
69A SER* 3.0 26.2 + - - -
73A SER* 1.3 71.9 - - - +
75A PHE* 1.3 64.2 + - - +
76A TRP* 3.9 9.1 - - - +
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Residues in contact with PHE 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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15A MET* 5.5 5.8 - - + -
27A ARG* 5.5 6.3 - - + -
28A LEU 3.5 4.0 - - - +
29A ARG* 3.7 30.1 - - + -
66A LYS* 3.5 3.3 - - - -
67A ILE* 2.8 28.2 + - + +
68A MET* 2.9 21.2 + - + +
69A SER* 4.5 0.4 - - - -
70A ASP* 3.7 31.4 - - + -
73A SER* 3.8 23.1 - - - -
74A ASP* 1.3 78.0 - - - +
76A TRP* 1.3 62.8 + - - +
418A SER 5.2 1.3 - - - -
419A HIS* 5.1 5.4 - + - -
422A MET* 3.6 57.2 - - + -
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Residues in contact with TRP 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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27A ARG* 3.0 9.9 - - - +
28A LEU* 2.9 43.3 + - + +
30A THR* 3.0 35.3 + - + +
35A ILE* 3.4 22.7 - - + -
36A VAL 3.6 24.0 - - - -
37A SER* 4.0 4.0 - - - -
38A VAL* 3.6 32.1 - - + -
64A MET* 3.8 29.8 - - + -
65A THR 3.2 8.3 - - - -
66A LYS* 3.4 50.9 - - + -
67A ILE* 4.6 0.9 - - - -
74A ASP* 3.9 7.3 - - - +
75A PHE* 1.3 78.6 - - - +
77A GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 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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25A ASN* 3.6 22.4 - - - +
26A ILE 3.2 14.8 - - - +
27A ARG* 2.8 38.3 + - + -
64A MET* 3.7 4.4 - - - +
65A THR* 2.9 33.8 + - - +
67A ILE* 3.6 29.5 - - + +
76A TRP* 1.3 76.2 - - - +
78A VAL* 1.3 70.6 + - - +
79A THR* 4.8 4.0 + - - -
426A ASP* 3.0 23.3 + - - +
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Residues in contact with VAL 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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24A VAL 4.1 0.2 - - - +
25A ASN* 3.6 2.4 - - - -
26A ILE* 2.9 37.5 + - + +
40A LEU* 3.8 28.7 - - + -
62A LYS* 4.5 15.9 - - + -
63A GLN 3.5 20.4 - - - +
64A MET* 3.8 24.7 - - + -
77A GLN* 1.3 79.8 - - - +
79A THR* 1.3 72.8 + - - +
80A VAL* 4.2 4.9 + - + -
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Residues in contact with THR 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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19A VAL* 5.3 0.2 - - + -
23A THR* 3.3 29.4 - - + -
24A VAL 3.4 6.7 - - - +
25A ASN* 2.9 17.7 + - - +
62A LYS* 5.8 1.2 - - - +
77A GLN* 4.8 4.3 + - - -
78A VAL* 1.3 86.4 - - - +
80A VAL* 1.3 64.5 + - - +
81A THR* 5.1 1.8 - - - +
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Residues in contact with VAL 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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22A GLN 3.9 0.2 - - - +
23A THR* 3.4 3.6 - - - +
24A VAL* 2.9 44.2 + - + +
26A ILE* 4.2 11.0 - - + -
40A LEU* 3.5 31.4 - - + -
42A ALA* 4.7 1.1 - - + -
62A LYS* 4.3 25.4 - - + +
78A VAL* 4.2 7.2 - - + +
79A THR* 1.3 79.1 - - - +
81A THR* 1.3 75.0 + - - +
82A GLU* 4.3 0.6 + - + +
87A LEU* 3.9 27.6 - - + -
128A PHE* 4.9 0.9 - - - -
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Residues in contact with THR 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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22A GLN* 3.2 27.4 - - + +
23A THR* 3.5 17.7 + - - +
62A LYS* 5.7 1.6 - - - -
79A THR* 5.1 1.9 - - - +
80A VAL* 1.3 80.6 - - - +
82A GLU* 1.3 70.2 + - - +
83A PRO* 4.3 8.0 - - + +
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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