Contacts of the helix formed by residues 99 - 106 (chain C) in PDB entry 1YV0
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 ASN 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C GLU* 2.9 43.4 + - - +
98C ALA* 1.3 77.8 - - - +
100C CYS* 1.3 57.9 + - - +
101C PHE 3.0 1.1 - - - -
102C ARG* 2.5 58.2 + - - +
103C ILE* 3.2 6.7 + - - +
29I ILE* 3.2 27.3 - - + +
229T ARG* 5.1 2.8 + - - -
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Residues in contact with CYS 100 (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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96C GLU* 3.1 16.5 + - - +
97C LEU* 5.1 3.8 - - + -
99C ASN* 1.3 80.8 - - - +
101C PHE* 1.3 63.2 + - - +
103C ILE* 2.9 2.0 + - - +
104C PHE* 2.8 49.3 + - + -
153C PHE* 3.6 11.2 - - + -
22I LEU* 4.1 21.3 - - + -
25I ALA* 4.1 21.5 - - - -
26I VAL* 5.1 5.8 - - - -
29I ILE* 5.2 4.3 - - - -
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Residues in contact with PHE 101 (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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98C ALA 3.8 8.7 - - - +
99C ASN 3.0 0.6 - - - -
100C CYS* 1.3 75.4 - - - +
102C ARG* 1.3 51.3 + - - +
105C ASP* 2.5 43.4 + - + +
110C GLY* 2.9 30.1 - - - -
112C ILE* 4.0 12.6 - - + -
148C ILE 3.7 11.7 - - - -
149C ASP* 4.6 0.2 - - - -
150C PHE* 3.1 62.6 - + + -
153C PHE* 3.1 46.7 - + + -
232T TYR* 4.5 8.7 - + + -
236T THR* 3.4 21.8 - - + -
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Residues in contact with ARG 102 (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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98C ALA 3.9 5.1 + - - +
99C ASN* 2.5 41.9 + - - +
101C PHE* 1.3 72.3 - - - +
103C ILE* 1.3 63.2 + - - +
104C PHE 3.1 4.9 + - - -
106C LYS* 2.7 43.4 + - - +
29I ILE* 4.5 18.2 + - - +
32I GLU* 2.9 34.7 + - - +
229T ARG* 3.4 45.7 - - - +
232T TYR* 3.5 36.6 + - + +
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Residues in contact with ILE 103 (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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99C ASN 3.2 6.7 + - - +
100C CYS 2.9 4.2 + - - +
102C ARG* 1.3 91.4 - - - +
104C PHE* 1.3 64.1 + - + +
106C LYS* 4.0 18.7 - - - +
120C ILE* 4.7 5.6 - - + +
24I LEU* 6.2 0.7 - - + -
25I ALA* 2.8 51.4 - - + +
28I GLU* 3.1 35.9 - - + +
29I ILE* 3.0 37.7 - - + +
32I GLU* 6.2 0.2 - - + -
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Residues in contact with PHE 104 (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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100C CYS* 2.8 40.3 + - + +
101C PHE 4.0 0.2 - - - +
103C ILE* 1.3 87.5 - - - +
105C ASP* 1.3 70.6 + - - +
106C LYS* 3.0 7.0 + - - +
112C ILE* 3.4 21.4 - - + +
116C GLU* 3.1 14.6 - - - +
120C ILE* 3.3 37.9 - - + -
153C PHE* 3.8 11.9 - + - -
157C MET* 4.8 0.2 - - - -
21I MET* 2.8 56.1 - - + -
22I LEU* 3.4 15.9 - - + -
25I ALA* 3.4 15.0 - - + -
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Residues in contact with ASP 105 (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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101C PHE* 2.5 27.8 + - + +
104C PHE* 1.3 71.2 - - - +
106C LYS* 1.3 57.3 + - - +
107C ASN* 2.4 25.3 - - - +
108C ALA 3.5 8.1 + - - -
109C ASP* 3.0 2.3 - - - +
110C GLY* 2.6 44.1 + - - +
111C PHE 2.7 13.9 + - - +
112C ILE* 3.1 18.0 - - + +
116C GLU* 2.7 12.0 - - - +
232T TYR* 2.7 34.9 + - - +
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Residues in contact with LYS 106 (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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102C ARG* 2.7 38.5 + - - +
103C ILE* 4.0 18.3 - - - +
104C PHE 3.0 9.8 - - - +
105C ASP* 1.3 81.7 + - - +
107C ASN* 1.3 73.1 + - - +
116C GLU* 2.8 10.6 - - - +
28I GLU* 4.9 16.6 + - - +
32I GLU* 4.5 21.9 + - - +
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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