Contacts of the strand formed by residues 58 - 67 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C LYS* 3.9 27.3 - - + -
29C LEU 3.2 2.7 + - - +
30C VAL* 3.5 26.2 - - + +
31C CYS 2.8 29.6 + - - -
56C CYS* 3.5 6.0 - - - +
57C SER* 1.3 111.7 + - - +
59C LEU* 1.3 59.4 + - - +
96C LYS* 3.3 30.2 - - + +
98C LEU* 4.2 15.0 - - + -
179C LEU* 4.2 9.7 - - + +
206C PHE* 4.0 23.2 - + - -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C CYS* 3.3 25.8 - - + +
33C PHE* 4.2 15.0 - - + -
51C ILE* 3.8 29.4 - - + -
52C ASP 5.4 2.0 - - - +
55C LEU* 6.3 0.2 - - + -
56C CYS* 4.3 8.3 - - + +
58C HIS* 1.3 74.4 - - - +
60C ILE* 1.3 60.3 + - - +
61C TYR 4.3 0.2 - - - -
88C LEU* 4.1 11.2 - - + -
95C LEU* 3.7 34.8 - - + -
96C LYS 2.8 9.3 + - - +
97C ILE* 3.2 11.7 - - + +
98C LEU* 2.7 32.6 + - - +
362C ILE* 4.1 17.7 - - + -
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.5 31.9 - - + -
31C CYS 2.9 11.7 + - - +
32C TYR* 3.4 28.5 - - + +
33C PHE* 2.9 35.1 + - - +
59C LEU* 1.3 79.5 - - - +
61C TYR* 1.3 61.3 + - - +
62C SER* 3.6 0.9 + - - -
98C LEU* 3.4 23.3 - - + +
100C SER* 3.5 35.0 - - - +
141C ASP* 4.0 12.6 - - + -
206C PHE* 5.7 0.7 - - + -
208C ASN* 3.7 17.0 - - - +
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Residues in contact with TYR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C PHE* 3.6 35.7 - + + -
35C ASN* 3.2 26.6 + - + +
48C PRO* 5.9 0.7 - - + -
60C ILE* 1.3 70.9 - - - +
62C SER* 1.3 59.5 + - - +
63C PHE 4.0 23.0 + - - -
73C ILE* 3.7 19.3 - - + +
74C LYS 4.5 0.9 + - - -
75C ASP* 2.6 35.3 + - - +
81C LEU* 3.5 31.2 - - + -
85C ILE* 6.1 0.2 - - + -
97C ILE* 5.3 0.6 - - + +
98C LEU 3.0 13.7 + - - +
99C LEU* 3.6 20.6 - - + -
100C SER* 2.9 29.1 + - - +
137C PHE* 4.4 9.6 - + + -
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Residues in contact with SER 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TYR* 3.2 30.5 - - - +
33C PHE 2.9 17.7 + - - -
34C THR* 3.3 3.6 - - - -
35C ASN* 2.8 33.4 + - - +
36C TRP* 3.7 3.9 - - - -
61C TYR* 1.3 79.5 - - - +
63C PHE* 1.3 79.3 + - - +
360C TRP* 3.6 13.5 - - - -
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Residues in contact with PHE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TYR* 5.0 1.3 - + - -
35C ASN* 4.5 11.7 + - - +
36C TRP* 3.9 23.3 - + + -
61C TYR* 4.0 12.3 + - - -
62C SER* 1.3 80.6 + - - +
64C ALA* 1.3 68.1 + - - +
74C LYS 5.3 4.7 + - - +
100C SER* 3.3 31.2 - - - +
102C GLY 3.3 31.0 - - - +
103C GLY* 3.4 23.6 - - - -
104C TYR 4.9 1.3 - - - -
106C PHE* 6.2 0.4 - - + -
143C SER* 4.6 6.3 - - - -
360C TRP* 3.6 35.0 - + - -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C PHE* 1.3 83.3 - - - +
65C SER* 1.3 60.2 + - - +
71C VAL* 3.9 9.4 - - + -
72C ILE 3.3 15.3 - - - +
73C ILE* 4.1 8.7 - - + +
99C LEU* 3.7 30.3 - - + +
100C SER 3.0 11.8 + - - +
101C ILE* 3.8 27.4 - - + +
102C GLY 4.4 1.4 + - - -
106C PHE* 4.5 5.0 - - - -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA* 1.3 76.5 - - - +
66C ILE* 1.3 76.9 + - - +
71C VAL* 3.4 9.5 - - - +
72C ILE* 2.8 38.0 + - - +
73C ILE* 4.9 0.4 - - - +
74C LYS* 3.4 34.8 + - - +
101C ILE* 4.4 1.1 - - - +
106C PHE* 3.6 18.9 - - - -
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C SER* 1.3 87.8 + - - +
67C GLU* 1.3 67.6 + - - +
68C ASN 4.4 0.4 + - - +
69C ASN* 3.7 34.5 - - - +
70C LYS 3.3 4.3 - - - +
74C LYS* 5.5 0.2 + - - -
101C ILE* 4.2 9.4 - - + -
106C PHE* 4.0 14.6 - - + -
110C GLY 3.9 26.2 - - - +
111C PHE* 4.1 11.4 - - + -
114C MET* 3.8 28.5 - - + -
124C PHE* 3.8 26.2 - - + -
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C SER 4.3 0.2 - - - -
66C ILE* 1.3 76.6 - - - +
68C ASN* 1.3 77.0 + - + +
69C ASN 3.1 0.4 - - - -
70C LYS* 2.9 23.4 + - - +
72C ILE* 3.3 37.1 - - + +
74C LYS* 3.3 23.6 + - - +
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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