Contacts of the helix formed by residues 62 - 72 (chain A) in PDB entry 1YSD
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 6.4 0.4 - - + -
51A ASN* 3.7 4.9 - - - +
53A ARG* 4.2 6.6 + - - -
59A ALA 5.1 0.4 - - - -
60A THR 2.8 12.6 + - - +
61A LEU* 1.3 77.2 - - - +
63A GLY* 1.3 60.6 + - - +
64A GLU* 3.2 2.9 - - - +
65A ILE* 3.1 2.4 + - + +
66A SER* 2.8 26.0 + - - -
91A CYS* 3.5 13.0 - - + -
93A MET* 3.6 9.3 - - + +
94A CYS* 3.6 12.3 - - - -
155A ASP* 2.7 57.2 + - - -
156A ILE* 4.9 3.4 - - + -
500A ZN 3.8 6.6 - - - -
501A ZN 2.1 38.3 - - - -
300B MET* 3.7 18.1 - - + +
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Residues in contact with GLY 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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33A ILE* 3.7 20.3 - - - +
34A GLY* 4.8 4.7 - - - -
49A GLY 4.0 2.6 - - - +
50A HIS* 3.7 2.9 - - - -
51A ASN* 3.5 28.3 - - - +
62A HIS* 1.3 72.4 - - - +
64A GLU* 1.3 62.1 + - - +
66A SER* 3.7 1.7 - - - -
67A THR* 2.9 33.9 + - - -
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Residues in contact with GLU 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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33A ILE* 4.0 3.7 - - - +
34A GLY 5.9 0.2 - - - +
35A GLY* 6.0 1.6 - - - -
63A GLY* 1.3 81.2 + - - +
65A ILE* 1.3 65.6 + - + +
67A THR* 3.3 8.3 + - - -
68A LEU* 3.1 29.3 + - + +
84A LEU* 4.3 22.0 - - + +
85A TYR 5.6 0.2 - - - +
86A THR* 3.3 37.0 + - + +
88A LEU 3.6 1.6 - - - +
90A PRO* 3.4 30.3 - - + +
94A CYS* 3.6 29.5 - - + +
97A ALA* 6.3 0.4 - - + -
98A ILE* 5.6 0.7 - - + -
500A ZN 3.6 16.2 - - - -
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Residues in contact with ILE 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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60A THR* 3.4 33.0 - - - +
61A LEU* 4.2 8.3 - - + -
62A HIS 3.1 5.0 + - - +
64A GLU* 1.3 74.5 - - - +
66A SER* 1.3 61.1 + - - +
68A LEU* 3.3 2.2 + - + -
69A GLU* 2.8 27.5 + - - +
93A MET* 3.9 17.5 - - + -
94A CYS* 3.8 25.6 - - - -
97A ALA* 3.9 28.3 - - + -
260B THR* 3.6 31.9 - - + +
265B ILE* 5.6 2.7 - - + -
293B MET* 4.7 8.1 - - - -
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Residues in contact with SER 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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50A HIS 3.0 35.1 + - - -
52A MET* 3.9 10.5 - - - +
61A LEU* 3.9 20.7 - - - +
62A HIS 2.8 15.2 + - - -
63A GLY 3.7 3.4 - - - -
65A ILE* 1.3 78.0 - - - +
67A THR* 1.3 61.6 + - - +
69A GLU* 3.2 2.2 + - - +
70A ASN* 2.9 40.9 + - - +
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Residues in contact with THR 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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35A GLY* 3.2 23.5 + - - +
36A CYS* 3.4 36.3 - - - +
37A LEU* 3.7 7.6 - - + +
47A GLY 3.9 5.6 - - - +
48A ARG 4.2 1.5 + - - -
49A GLY 3.4 13.7 + - - +
63A GLY 2.9 20.6 + - - -
64A GLU* 3.4 11.4 - - - -
65A ILE 3.2 0.2 - - - -
66A SER* 1.3 75.6 - - - +
68A LEU* 1.3 62.7 + - - +
70A ASN* 3.2 12.5 + - - +
71A CYS* 3.3 13.5 + - - -
84A LEU* 3.8 11.9 - - + -
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Residues in contact with LEU 68 (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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37A LEU* 4.2 21.1 - - + -
64A GLU* 3.1 20.1 + - + +
65A ILE* 3.7 7.0 - - - +
67A THR* 1.3 74.2 - - - +
69A GLU* 1.3 66.2 + - - +
71A CYS* 3.1 19.0 + - - +
72A GLY 3.7 3.5 + - - -
79A TYR* 4.3 12.7 + - + -
84A LEU* 4.7 13.2 - - + -
97A ALA* 3.8 31.6 - - + -
98A ILE 5.1 0.4 - - - +
101A TYR* 4.3 18.4 - - + -
103A ILE* 3.8 26.5 - - + -
259B ALA* 4.0 11.0 - - + +
260B THR* 4.0 14.4 - - + -
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Residues in contact with GLU 69 (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 LEU* 4.4 13.0 - - + -
65A ILE 2.8 17.4 + - - +
66A SER* 3.5 9.0 - - - +
68A LEU* 1.3 77.1 - - - +
70A ASN* 1.3 66.4 + - - +
72A GLY* 3.2 15.1 + - - -
256B LYS* 5.1 2.3 - - - +
257B GLY 4.8 2.6 - - - +
258B SER* 2.8 36.7 + - - -
259B ALA* 3.4 3.8 + - - -
260B THR* 2.7 35.1 + - - +
261B LEU* 4.3 7.2 - - - +
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Residues in contact with ASN 70 (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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46A LEU 4.3 3.3 - - - +
47A GLY* 4.6 3.5 - - - -
48A ARG 2.8 32.0 + - - +
49A GLY* 3.7 9.5 - - - -
66A SER* 2.9 27.6 + - - +
67A THR 3.6 4.0 - - - +
68A LEU 3.2 0.4 - - - -
69A GLU* 1.3 81.3 - - - +
71A CYS* 1.3 61.1 + - - +
72A GLY* 3.2 0.8 + - - -
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Residues in contact with CYS 71 (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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37A LEU* 3.7 31.2 - - + -
46A LEU* 3.5 15.4 - - - +
47A GLY* 3.6 24.5 - - - -
67A THR 3.3 15.0 + - - -
68A LEU* 3.1 13.5 + - - +
70A ASN* 1.3 78.7 - - - +
72A GLY* 1.3 62.9 + - - +
73A ARG 4.9 0.2 - - - +
74A LEU* 4.0 29.9 - - + +
79A TYR* 5.4 2.5 - - + +
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Residues in contact with GLY 72 (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 LEU 3.7 1.2 + - - -
69A GLU 3.2 15.2 + - - -
70A ASN 3.2 1.4 - - - -
71A CYS* 1.3 83.7 - - - +
73A ARG* 1.3 65.7 + - - -
74A LEU* 3.3 7.8 + - - +
79A TYR* 3.8 2.9 + - - -
257B GLY 4.4 8.5 - - - -
259B ALA* 3.7 18.1 - - - +
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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