Contacts of the helix formed by residues 65 - 77 (chain C) in PDB entry 5SY1
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 ASP 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A SER 4.4 0.3 - - - +
626A ARG* 3.4 37.4 + - - +
629A PHE* 3.0 31.1 - - - +
630A GLN* 3.9 8.5 - - + +
17C PHE* 4.2 2.4 - - - -
26C GLY 4.0 5.4 - - - +
27C THR* 4.7 0.7 - - - -
59C ASP* 5.5 0.7 - - - +
64C ILE* 1.3 79.6 - - - +
66C PHE* 1.3 78.3 + - - +
67C PRO* 3.5 11.4 - - + +
68C GLU* 2.9 29.2 + - + +
69C PHE* 2.8 23.6 + - - +
204C CA 3.9 3.0 - - - -
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Residues in contact with PHE 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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622A LEU* 4.0 29.6 - - + -
625A SER* 5.2 5.4 - - - +
629A PHE* 6.0 3.1 - - + -
10C ILE* 4.3 13.0 - - + -
13C PHE* 3.2 37.2 - - + -
14C LYS* 3.6 42.6 - - - +
17C PHE* 3.8 37.0 - + + -
26C GLY 4.3 0.9 + - - +
65C ASP* 1.3 80.3 + - - +
67C PRO* 1.3 69.4 - - + +
69C PHE* 3.0 12.8 + + - +
70C LEU* 2.8 33.5 + - + +
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Residues in contact with PRO 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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612A LEU* 4.3 8.8 - - + +
615A THR* 5.6 6.3 - - + -
616A LEU* 4.7 13.2 - - + -
622A LEU* 4.6 16.2 - - + +
625A SER 4.7 2.5 - - - +
626A ARG* 3.9 35.4 - - + +
65C ASP* 3.5 18.2 - - - +
66C PHE* 1.3 96.1 - - + +
68C GLU* 1.3 62.9 + - - +
70C LEU* 3.8 9.9 - - + +
71C THR* 3.3 30.5 + - + +
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Residues in contact with GLU 68 (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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612A LEU* 4.5 18.4 - - + +
626A ARG* 5.4 5.4 + - - +
56C VAL* 3.6 26.7 - - - +
57C ASP* 3.0 12.0 - - - +
58C ALA* 4.2 7.2 - - + +
59C ASP* 2.6 25.3 + - - +
63C THR 3.1 3.1 - - - +
64C ILE* 3.3 6.5 - - + -
65C ASP* 2.9 30.7 + - + +
66C PHE 3.2 0.6 - - - -
67C PRO* 1.3 78.5 - - + +
69C PHE* 1.3 62.1 + - - +
71C THR* 3.3 16.2 + - - -
72C MET* 3.6 4.9 - - - +
116C LYS* 5.2 1.2 + - - -
204C CA 2.4 31.6 - - - -
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Residues in contact with PHE 69 (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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559A VAL* 5.2 4.3 - - + -
560A MET* 5.8 0.2 - - - -
563A PHE* 3.6 55.0 - + + -
13C PHE* 3.9 35.7 - + + -
16C ALA* 4.9 7.6 - - + -
17C PHE* 3.9 33.7 - + + -
20C PHE* 4.3 15.0 - + - -
28C ILE* 5.2 4.3 - - + -
56C VAL* 4.8 2.5 - - - -
64C ILE* 4.1 7.6 - - + +
65C ASP 2.8 14.2 + - - +
66C PHE* 3.0 15.0 + + - +
68C GLU* 1.3 76.0 - - - +
70C LEU* 1.3 65.9 - - - +
71C THR 3.5 0.2 + - - -
72C MET* 3.7 10.2 + - - +
73C MET* 3.9 16.1 + - + +
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Residues in contact with LEU 70 (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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615A THR* 3.9 26.5 - - + -
619A ASN* 4.6 5.8 - - - +
622A LEU* 4.1 20.9 - - + -
2C ALA 5.9 2.5 - - - +
5C LEU* 4.7 15.0 - - + -
10C ILE* 5.5 3.8 - - + -
13C PHE* 3.5 39.9 - - + -
66C PHE* 2.8 25.8 + - + +
67C PRO* 3.8 8.5 - - + +
68C GLU 3.3 0.8 - - - -
69C PHE* 1.3 80.8 - - - +
71C THR* 1.3 59.1 + - + +
72C MET 3.3 0.2 + - - -
73C MET* 3.4 6.4 + - + +
74C ALA* 3.0 30.2 + - + +
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Residues in contact with THR 71 (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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611A GLN* 3.9 20.0 - - + +
612A LEU* 4.5 11.2 - - + +
615A THR* 3.5 29.4 - - + +
2C ALA* 6.0 0.7 - - + -
56C VAL 5.5 1.0 + - - -
67C PRO* 3.3 14.3 + - + +
68C GLU* 3.3 14.6 + - - -
70C LEU* 1.3 74.7 - - - +
72C MET* 1.3 67.3 + - - +
74C ALA* 3.6 8.5 - - + +
75C ARG* 3.0 46.5 + - - +
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Residues in contact with MET 72 (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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563A PHE* 4.2 14.6 - - + -
566A LEU* 3.9 21.0 - - + +
567A LEU* 4.7 10.8 - - + -
55C GLU* 4.2 28.7 - - + +
56C VAL* 3.7 45.3 - - + +
68C GLU 3.6 16.4 - - - +
69C PHE 3.7 6.9 + - - +
70C LEU 3.2 0.6 - - - -
71C THR* 1.3 80.1 + - - +
73C MET* 1.3 63.6 + - - +
75C ARG* 2.8 41.7 + - - +
76C LYS* 4.1 14.9 + - - +
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Residues in contact with MET 73 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A VAL* 3.9 41.3 - - + +
233A LEU* 4.6 3.6 - - - +
559A VAL* 4.5 4.7 - - + +
562A ALA 4.0 17.5 - - - +
563A PHE* 3.4 39.9 - - + +
566A LEU* 3.8 16.4 - - - -
13C PHE* 4.9 18.4 - - + -
69C PHE* 3.9 18.8 + - + +
70C LEU* 3.4 7.4 + - + +
71C THR 3.3 0.2 - - - -
72C MET* 1.3 74.9 - - - +
74C ALA* 1.3 59.7 + - - +
75C ARG 3.4 0.6 + - - -
76C LYS 4.5 0.4 - - - -
77C MET* 4.0 36.3 + - + +
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Residues in contact with ALA 74 (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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233A LEU* 3.9 12.2 - - + +
615A THR* 5.4 0.2 - - - +
2C ALA* 3.4 36.6 + - + +
70C LEU* 3.0 23.9 + - + +
71C THR* 3.6 10.8 - - - +
72C MET 3.2 0.4 - - - -
73C MET* 1.3 78.9 - - - +
75C ARG* 1.3 66.1 + - - +
77C MET 4.7 0.2 - - - -
78C LYS* 3.6 22.3 - - - +
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Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604A LYS* 5.3 15.0 - - - +
608A ALA* 4.2 22.8 + - - +
611A GLN* 2.6 39.1 + - - +
2C ALA* 6.2 0.2 - - - -
55C GLU 5.0 5.0 + - - -
56C VAL 5.6 2.2 + - - -
71C THR* 3.0 30.0 + - - +
72C MET* 2.8 50.4 - - - +
73C MET 3.4 0.8 - - - -
74C ALA* 1.3 80.2 - - + +
76C LYS* 1.3 84.7 + - + +
77C MET 3.6 0.9 + - - -
78C LYS* 3.8 12.7 + - - +
148C SER 6.0 1.6 - - - -
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ARG* 6.0 0.9 - - - +
230A LYS* 4.8 3.8 + - - -
566A LEU* 3.9 33.9 + - + +
570A SER* 4.7 14.3 - - - -
55C GLU* 3.8 20.4 + - - -
72C MET* 4.1 14.6 + - - +
73C MET 4.2 0.8 + - - -
74C ALA 3.6 0.2 - - - -
75C ARG* 1.3 99.0 - - + +
77C MET* 1.3 75.1 + - - +
78C LYS 3.5 1.9 - - - +
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Residues in contact with MET 77 (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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226A ARG* 4.1 43.3 - - + +
229A VAL* 4.2 13.2 - - + +
230A LYS* 3.7 42.4 - - - +
233A LEU* 4.3 9.8 - - + +
234A LYS* 5.5 1.6 + - - +
562A ALA* 4.8 5.2 - - + +
566A LEU* 3.6 44.0 - - + -
73C MET* 4.0 34.3 + - + +
75C ARG 3.5 0.2 - - - -
76C LYS* 1.3 86.1 - - + +
78C LYS* 1.3 65.1 + - - +
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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