Contacts of the helix formed by residues 60 - 71 (chain C) in PDB entry 5IYB
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 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740B PHE* 6.1 2.9 - + - -
752B TYR* 3.5 31.5 - + - -
809B VAL* 3.5 23.0 - - + +
811B TYR* 3.8 15.7 - - - +
924B ARG* 3.0 47.7 + - - +
926B VAL* 4.1 6.3 - - + -
55C ASN* 4.1 0.2 - - - -
59C LEU* 1.3 77.9 - - - +
61C ASP* 1.3 62.8 + - - +
62C GLU* 3.8 2.3 + - + -
63C PHE* 2.9 49.8 + + + +
64C ILE* 3.3 5.4 + - - +
1J MET* 6.3 0.9 - - - -
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Residues in contact with ASP 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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903B ILE* 5.8 0.4 - - - -
924B ARG* 3.6 21.0 + - - +
52C ILE* 3.3 23.9 - - + +
55C ASN* 3.0 29.0 + - - +
60C HIS* 1.3 78.9 + - - +
62C GLU* 1.3 57.5 + - + +
64C ILE* 3.2 3.9 + - - +
65C ALA* 3.2 20.4 + - - +
48L ARG* 2.5 44.8 + - - -
55L PHE* 4.3 14.3 - - + -
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B TYR* 4.6 3.2 + - - +
859B ARG* 5.4 2.6 + - - -
903B ILE* 3.7 16.9 - - - +
924B ARG* 4.0 14.7 - - - +
925B SER* 5.4 0.2 - - - -
926B VAL* 3.0 39.1 + - + +
60C HIS* 3.8 7.9 + - + -
61C ASP* 1.3 72.0 - - - +
63C PHE* 1.3 60.8 + - - +
64C ILE 3.2 0.7 - - - -
65C ALA* 3.7 7.8 - - + +
66C HIS* 2.9 30.7 + - - +
55L PHE* 3.1 40.7 - - + -
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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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752B TYR* 3.6 45.3 - + + -
753B TYR* 3.2 35.4 - + - -
59C LEU* 3.9 26.7 - - + -
60C HIS* 2.9 46.6 + + + +
62C GLU* 1.3 79.9 - - - +
64C ILE* 1.3 59.2 + - - +
66C HIS* 3.5 4.9 + - - +
67C ARG* 3.2 30.7 + - + +
1J MET* 3.7 32.5 - - + -
2J ILE* 4.5 2.0 - - + -
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Residues in contact with ILE 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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52C ILE* 4.6 3.8 - - + -
55C ASN* 3.3 39.7 - - - +
57C SER* 3.9 12.3 - - - +
59C LEU* 4.2 15.5 - - + +
60C HIS 3.3 5.1 + - - +
61C ASP 3.2 8.3 + - - +
63C PHE* 1.3 75.2 - - - +
65C ALA* 1.3 65.1 + - - +
67C ARG* 3.3 7.6 + - - +
68C LEU* 3.1 31.4 + - + +
150C ILE* 4.6 9.4 - - + +
151C VAL* 5.0 5.6 - - + -
159C LEU* 3.9 22.0 - - + -
161C LEU* 4.0 25.6 - - + -
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C VAL* 4.4 15.9 - - + +
52C ILE* 5.0 0.4 - - + +
61C ASP 3.2 9.9 + - - +
62C GLU* 3.4 9.8 + - + +
64C ILE* 1.3 79.8 - - - +
66C HIS* 1.3 61.5 + - - +
68C LEU* 3.6 10.6 + - - +
69C GLY 3.2 16.5 + - - -
55L PHE* 4.0 27.4 - - + -
56L ASP 4.6 8.5 - - - +
57L ALA* 3.4 14.9 - - - +
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Residues in contact with HIS 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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752B TYR* 4.3 11.0 - + + +
753B TYR* 3.6 26.8 + + - -
802B ASP 3.8 3.6 + - - -
803B ARG 3.7 7.9 - - - -
804B GLY* 3.3 38.4 + - - -
807B ARG* 3.6 33.4 - - - +
62C GLU 2.9 18.5 + - - +
63C PHE* 3.6 6.4 + - - +
64C ILE 3.2 0.2 - - - -
65C ALA* 1.3 75.1 - - - +
67C ARG* 1.3 67.2 + - - +
69C GLY* 3.2 9.9 + - - -
70C LEU* 3.4 25.8 + - + +
173C HIS* 5.9 0.9 - + - -
57L ALA 3.7 15.5 + - - +
58L ARG 5.0 0.9 - - - +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B TYR* 3.5 22.8 + - - -
59C LEU* 4.8 1.9 - - + +
63C PHE* 3.2 21.8 + - + +
64C ILE* 3.3 6.9 + - - +
66C HIS* 1.3 77.6 - - - +
68C LEU* 1.3 63.1 + - - +
70C LEU* 3.3 14.8 + - - +
71C ILE* 3.7 15.3 + - - +
148C ILE* 3.4 11.2 - - + +
149C LEU 2.7 28.5 + - - -
150C ILE* 4.1 24.6 + - + +
2J ILE* 3.1 42.6 + - - +
3J ILE 2.7 26.2 + - - -
5J VAL* 3.2 23.7 - - + +
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Residues in contact with LEU 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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47C ILE* 3.5 18.0 - - + +
50C VAL* 3.8 30.1 - - + -
64C ILE* 3.1 23.0 + - + +
65C ALA 3.6 4.5 - - - +
67C ARG* 1.3 77.0 - - - +
69C GLY* 1.3 66.5 + - - +
71C ILE* 3.0 25.9 - - + +
103C LEU* 5.4 3.4 - - + -
120C LEU* 4.2 24.0 - - + -
150C ILE* 3.9 31.0 - - + -
161C LEU* 3.9 30.7 - - + -
163C ALA* 5.0 2.2 - - + -
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Residues in contact with GLY 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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46C ALA* 4.3 2.9 - - - +
47C ILE* 3.9 18.6 + - - +
65C ALA 3.2 11.5 + - - -
66C HIS 3.2 4.3 + - - -
68C LEU* 1.3 78.2 - - - +
70C LEU* 1.3 62.2 + - - +
71C ILE 3.3 7.4 + - - +
175C LYS* 4.0 18.0 - - - +
6J ARG* 5.3 0.2 + - - -
57L ALA* 3.6 25.3 - - - +
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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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802B ASP 4.8 3.6 - - - +
803B ARG* 3.7 40.8 - - + +
66C HIS* 3.7 29.8 - - + +
67C ARG* 3.3 9.5 + - - +
68C LEU 3.2 1.0 - - - -
69C GLY* 1.3 74.1 - - - +
71C ILE* 1.3 61.6 + - - +
72C PRO* 3.4 1.6 - - - +
173C HIS* 5.4 2.9 - - + -
175C LYS* 4.0 27.1 - - + +
5J VAL* 4.0 30.5 - - + +
6J ARG* 3.0 43.0 + - - +
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ALA* 4.9 5.2 - - - +
47C ILE* 3.7 15.5 + - + -
67C ARG 3.7 13.2 + - - +
68C LEU* 3.0 17.9 - - + +
69C GLY 3.6 6.2 - - - +
70C LEU* 1.3 75.9 - - - +
72C PRO* 1.3 73.6 - - + +
73C LEU* 3.9 12.8 + - + +
117C SER* 4.4 3.6 - - - +
120C LEU* 3.7 29.4 - - + -
130C VAL* 3.9 17.5 - - + -
147C ASP* 3.8 6.3 - - - +
148C ILE* 3.5 33.7 - - + -
150C ILE* 5.4 4.3 - - + -
5J VAL* 4.5 4.7 - - + -
6J ARG* 5.0 0.7 + - - -
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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