Contacts of the helix formed by residues 59 - 70 (chain C) in PDB entry 1Y1V
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 ALA 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786B ASN* 6.2 0.2 - - - +
854B LEU* 5.1 13.8 - - + +
856B PHE* 6.0 2.0 - - + -
950B ASP* 5.0 2.7 - - - +
969B ARG* 3.8 24.9 - - + +
54C ASN* 4.6 1.6 - - - +
57C VAL 3.5 3.2 + - - +
58C LEU* 1.3 73.5 - - - +
60C ASP* 1.3 58.7 + - - +
61C GLU* 3.5 13.9 - - - +
62C PHE* 2.7 46.6 + - + +
63C ILE* 3.2 3.5 + - - -
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Residues in contact with ASP 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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948B ILE* 6.0 0.2 - - - -
969B ARG* 3.2 20.4 + - - -
51C VAL* 3.7 19.5 - - + +
54C ASN* 3.2 22.5 + - - +
59C ALA* 1.3 67.4 - - - +
61C GLU* 1.3 58.5 + - - +
63C ILE* 2.8 14.9 + - - +
64C ALA* 2.7 32.7 + - - +
60L ARG* 2.4 39.0 + - - -
67L PHE* 3.2 27.6 - - + -
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B TYR* 3.4 8.3 - - - +
854B LEU* 5.0 1.6 - - - -
948B ILE* 4.1 5.9 - - + +
969B ARG* 3.0 49.1 + - - -
970B THR* 4.6 0.7 - - - -
971B THR* 3.1 30.5 + - + +
59C ALA* 3.5 4.5 - - - -
60C ASP* 1.3 86.7 + - - +
62C PHE* 1.3 57.8 + - + +
64C ALA* 3.1 13.1 - - + +
65C HIS* 2.6 35.7 + - - +
67L PHE* 3.5 18.2 - - + -
68L GLU* 4.8 11.0 - - - +
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Residues in contact with PHE 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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797B TYR* 4.1 38.6 - + + -
798B TYR* 3.2 47.1 - + - -
854B LEU* 5.2 8.7 - - + -
58C LEU* 3.3 32.1 - - + -
59C ALA* 2.7 33.1 + - + +
61C GLU* 1.3 81.3 - - + +
63C ILE* 1.3 56.2 + - - +
65C HIS* 3.1 4.3 - + - +
66C ARG* 2.9 37.8 + - + +
1J MET* 3.7 33.0 - - - -
2J ILE* 4.9 0.4 - - + -
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Residues in contact with ILE 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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54C ASN* 4.0 18.2 - - + +
56C THR* 4.0 8.7 - - - +
58C LEU* 3.9 38.4 - - + +
59C ALA 4.1 6.7 - - - +
60C ASP* 2.8 10.7 + - - +
62C PHE* 1.3 69.9 - - - +
64C ALA* 1.3 71.6 + - - +
66C ARG* 2.7 22.7 + - + +
67C LEU* 2.9 37.2 + - + +
144C ILE* 4.2 13.9 - - + +
145C CYS* 5.1 7.4 - - + -
153C LEU* 4.5 17.3 - - + -
155C LEU* 4.1 13.0 - - + -
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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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49C VAL* 4.3 19.2 - - + +
60C ASP 2.7 11.4 + - - +
61C GLU* 3.1 24.0 - - - +
63C ILE* 1.3 76.1 - - - +
65C HIS* 1.3 63.6 + - - +
67C LEU* 3.1 26.5 + - - +
68C GLY* 3.2 4.5 + - - -
155C LEU* 5.5 0.4 - - - +
67L PHE* 4.1 14.6 - - + -
68L GLU 3.9 19.5 - - - +
69L ALA* 4.6 3.4 - - - +
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Residues in contact with HIS 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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797B TYR* 4.6 12.3 - + + -
798B TYR* 4.1 19.4 + + - -
847B ASP 3.0 27.8 - - - -
848B ARG 4.0 3.2 + - - -
849B GLY* 3.5 20.1 + - - -
852B ARG* 3.4 32.7 + - - +
61C GLU 2.6 15.5 + - - +
62C PHE* 3.1 12.6 - - - +
64C ALA* 1.3 73.4 - - - +
66C ARG* 1.3 66.7 + - - +
68C GLY* 3.0 9.5 + - - -
69C LEU* 2.8 40.8 - - + +
167C HIS* 5.3 0.9 - - - -
68L GLU 4.7 0.6 + - - -
69L ALA 4.1 3.2 + - - +
70L ARG* 4.0 17.1 + - - +
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Residues in contact with ARG 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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798B TYR* 3.2 14.0 + - - +
58C LEU* 4.9 4.3 - - - -
62C PHE* 2.9 36.8 - - + +
63C ILE* 2.7 21.7 + - - +
65C HIS* 1.3 73.8 - - - +
67C LEU* 1.3 68.3 + - + +
69C LEU* 3.0 25.4 + - - +
70C ILE* 3.3 8.8 + - + +
143C LEU 3.3 22.4 + - - -
144C ILE* 3.3 23.1 + - + +
2J ILE* 3.0 25.2 - - - +
3J VAL 2.7 22.6 + - - -
4J PRO* 3.6 1.6 - - - +
5J VAL* 2.8 43.7 - - + +
15J GLY* 5.5 1.6 - - - -
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Residues in contact with LEU 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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46C ILE* 3.9 26.1 - - + +
49C VAL* 3.9 8.5 - - + -
63C ILE* 2.9 16.5 + - + +
64C ALA* 3.2 7.2 - - - +
66C ARG* 1.3 71.1 - - - +
68C GLY* 1.3 70.5 + - - +
70C ILE* 2.8 45.1 + - + +
101C LEU* 4.8 4.9 - - + -
118C LEU* 5.6 1.8 - - + -
144C ILE* 3.4 31.6 - - + -
155C LEU* 3.1 36.1 - - + -
157C CYS* 3.7 15.9 - - - -
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Residues in contact with GLY 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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45C ALA* 3.6 22.9 - - - +
46C ILE* 3.5 24.9 + - - +
64C ALA 3.2 4.0 + - - -
65C HIS 3.0 10.0 + - - -
67C LEU* 1.3 78.7 - - - +
69C LEU* 1.3 63.4 + - - +
70C ILE 3.6 2.1 - - - +
169C LYS* 3.9 11.2 - - - +
69L ALA* 3.9 13.2 - - - -
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Residues in contact with LEU 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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798B TYR* 6.0 1.6 - - + +
847B ASP 4.9 0.9 - - - +
848B ARG* 4.1 27.6 - - + +
65C HIS* 2.8 54.7 - - + +
66C ARG* 3.0 8.0 + - - +
68C GLY* 1.3 74.7 - - - +
70C ILE* 1.3 66.6 + - - +
71C PRO* 2.8 7.8 - - - +
167C HIS* 5.3 2.2 - - - +
169C LYS* 4.1 20.2 - - + +
5J VAL* 3.4 42.4 - - + +
6J ARG* 3.0 32.0 + - + +
69L ALA 5.2 1.6 - - - +
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Residues in contact with ILE 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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45C ALA* 4.8 1.9 - - - +
46C ILE* 4.8 1.3 - - + -
66C ARG 3.3 4.9 + - - +
67C LEU* 2.8 47.6 + - + +
68C GLY 3.6 6.2 - - - +
69C LEU* 1.3 69.3 - - - +
71C PRO* 1.3 84.5 - - + +
72C LEU* 3.2 16.5 + - + +
115C SER* 3.5 24.9 - - - +
118C LEU* 4.5 15.9 - - + -
132C PRO* 4.8 3.6 - - + -
133C ILE 5.8 0.2 - - - +
142C VAL* 4.1 16.2 - - + -
144C ILE* 3.2 33.9 - - + -
5J VAL* 4.2 3.5 - - + +
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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