Contacts of the strand formed by residues 58 - 67 (chain A) in PDB entry 4AY1
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.8 28.7 - - + +
29A LEU 3.2 3.0 + - - +
30A VAL* 4.1 21.3 - - + +
31A CYS 2.8 24.4 + - - -
56A CYS* 3.6 6.2 - - - +
57A SER* 1.3 112.0 + - - +
59A LEU* 1.3 64.2 + - - +
96A LYS* 3.2 33.6 - - + +
98A LEU* 4.1 15.0 - - + -
179A LEU* 4.4 9.0 - - + +
206A PHE* 4.0 25.0 - + - -
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Residues in contact with LEU 59 (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 CYS* 3.3 23.1 - - + +
33A PHE* 4.0 15.0 - - + -
51A ILE* 3.7 35.0 - - + -
52A ASP 5.4 1.6 - - - +
56A CYS* 4.2 9.4 - - + -
58A HIS* 1.3 74.9 - - - +
60A ILE* 1.3 66.4 + - - +
61A TYR 4.3 0.4 - - - -
88A LEU* 4.0 9.0 - - + -
95A LEU* 3.8 33.2 - - + -
96A LYS 2.9 7.3 + - - +
97A ILE* 3.4 17.8 - - + -
98A LEU* 2.8 26.9 + - - +
362A ILE* 4.2 12.3 - - + -
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.4 32.8 - - + -
31A CYS 2.8 10.7 + - - +
32A TYR* 3.3 37.4 - - + +
33A PHE* 2.9 32.7 + - - +
59A LEU* 1.3 81.3 - - - +
61A TYR* 1.3 60.6 + - - +
62A SER* 3.7 1.2 + - - -
98A LEU* 3.5 22.9 - - + +
100A SER* 3.6 21.1 - - - +
141A ASP* 4.0 13.0 - - + -
181A THR* 4.7 2.5 - - - +
206A PHE* 5.5 0.9 - - + -
208A ASN* 3.6 19.3 - - - +
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Residues in contact with TYR 61 (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 PHE* 3.6 36.3 - + + -
35A ASN* 3.1 34.2 + - + -
48A PRO* 6.1 1.3 - - + -
59A LEU 4.3 0.2 - - - -
60A ILE* 1.3 71.0 - - - +
62A SER* 1.3 61.3 + - - +
63A PHE 3.9 21.3 + - - -
73A ILE* 3.5 20.5 - - + +
75A ASP* 2.6 35.1 + - - +
81A LEU* 3.7 26.0 - - + -
97A ILE* 5.5 1.5 - - + +
98A LEU 3.1 14.8 + - - +
99A LEU* 3.6 19.3 - - + -
100A SER* 2.9 31.7 + - - +
137A PHE* 4.7 7.9 - - + -
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Residues in contact with SER 62 (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 TYR* 3.2 30.0 - - - -
33A PHE 2.9 14.6 + - - -
34A THR* 3.4 5.6 - - - -
35A ASN* 2.8 33.8 + - - +
36A TRP* 3.8 3.4 - - - -
61A TYR* 1.3 78.5 + - - +
63A PHE* 1.3 81.3 + - - +
100A SER* 4.3 0.2 - - - -
360A TRP* 3.6 12.4 - - - -
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Residues in contact with PHE 63 (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 TYR* 5.1 1.1 - + - -
35A ASN* 4.5 8.2 + - - +
36A TRP* 3.8 31.9 - + - -
61A TYR* 3.9 14.6 + - - -
62A SER* 1.3 82.0 + - - +
64A ALA* 1.3 68.9 + - - +
74A LYS* 5.4 7.1 + - - +
100A SER* 3.4 29.4 - - - +
102A GLY 3.2 28.7 - - - +
103A GLY* 3.4 27.6 - - - -
104A TYR 5.1 0.9 - - - -
106A PHE* 6.4 0.4 - - + -
143A SER* 4.6 6.7 - - - -
360A TRP* 3.6 23.3 - + - -
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Residues in contact with ALA 64 (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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61A TYR* 4.3 2.6 - - - -
63A PHE* 1.3 83.5 - - - +
65A SER* 1.3 61.8 + - - +
71A VAL* 3.8 10.8 - - + -
72A ILE 3.6 12.3 - - - +
73A ILE* 4.2 9.4 - - + +
99A LEU* 3.7 35.9 - - + +
100A SER 2.8 12.0 + - - +
101A ILE* 3.8 19.6 - - + +
102A GLY 4.5 1.2 + - - -
106A PHE* 4.8 3.6 - - - -
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Residues in contact with SER 65 (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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63A PHE 5.5 0.2 - - - -
64A ALA* 1.3 75.6 - - - +
66A ILE* 1.3 69.2 + - - +
71A VAL* 3.5 8.3 - - - +
72A ILE* 2.8 49.9 + - - +
73A ILE* 4.9 0.2 - - - +
74A LYS* 3.7 35.0 + - - +
101A ILE* 4.8 0.8 - - - +
106A PHE* 4.2 18.4 - - - -
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Residues in contact with ILE 66 (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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65A SER* 1.3 84.6 - - - +
67A GLU* 1.3 64.4 + - - +
69A ASN* 3.8 31.6 - - - +
70A LYS 3.4 4.5 - - - +
72A ILE* 4.5 0.8 - - - +
101A ILE* 3.8 24.9 - - + -
106A PHE* 4.1 4.8 - - + -
110A GLY 3.9 23.4 - - - +
111A PHE* 4.3 5.4 - - + -
113A PRO* 6.3 1.6 - - + -
114A MET* 3.8 39.0 - - + -
124A PHE* 3.8 18.2 - - + -
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Residues in contact with GLU 67 (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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66A ILE* 1.3 75.4 - - - +
68A ASN* 1.3 87.5 + - - +
69A ASN 3.2 0.4 - - - -
70A LYS* 2.9 23.6 + - - +
72A ILE* 3.7 37.8 - - + +
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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