Contacts of the helix formed by residues 135 - 149 (chain C) in PDB entry 1Y8Q
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 SER 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLU* 5.1 0.7 + - - -
133C CYS 4.2 0.2 + - - -
134C CYS* 1.3 76.7 - - - +
136C ARG* 1.3 65.9 + - - +
137C ASP* 3.6 8.3 + - - +
138C VAL* 3.0 29.3 + - - +
139C ILE* 2.9 21.2 + - - +
250C ARG* 4.0 17.2 - - - +
251C THR* 5.1 10.1 - - - -
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Residues in contact with ARG 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C CYS 3.9 1.0 + - - -
135C SER* 1.3 71.7 - - - +
137C ASP* 1.3 73.0 + - - +
139C ILE* 3.3 8.5 + - - +
140C VAL* 3.0 37.7 + - + +
217C LYS* 4.5 5.3 + - - +
220C LEU* 3.6 39.9 + - + +
221C GLU* 3.3 41.2 + - - +
244C GLN* 4.1 16.0 - - - +
247C LEU* 4.2 30.5 + - + +
251C THR* 4.2 16.6 + - - +
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Residues in contact with ASP 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 6.1 0.7 - - - +
135C SER* 3.1 8.6 + - - +
136C ARG* 1.3 90.6 - - - +
138C VAL* 1.3 58.6 + - + +
140C VAL* 3.5 5.0 + - - +
141C LYS* 3.0 28.9 + - - +
251C THR* 5.3 10.5 + - - +
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE* 3.7 26.5 - - + -
116C GLU* 3.5 38.1 - - + +
131C LEU* 4.2 1.8 - - + -
134C CYS* 3.9 19.3 - - + -
135C SER* 3.0 25.1 + - - +
137C ASP* 1.3 73.9 - - + +
139C ILE* 1.3 67.6 + - - +
141C LYS* 3.2 6.1 + - - -
142C VAL* 2.8 39.6 + - + +
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU* 3.6 9.6 - - + -
134C CYS* 3.9 26.2 - - + +
135C SER 2.9 16.7 + - - +
136C ARG* 3.5 8.7 - - - +
138C VAL* 1.3 76.2 - - - +
140C VAL* 1.3 63.7 + - + +
143C ASP* 3.1 22.0 + - - +
153C PHE* 3.4 16.1 - - + -
155C THR* 3.3 27.1 - - + +
157C ASP* 5.1 3.1 - - - +
164C TYR* 3.8 13.7 - - - +
216C VAL* 3.9 27.1 - - + -
220C LEU* 5.0 3.8 - - + -
247C LEU* 4.3 18.2 - - + -
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ARG* 3.0 34.3 + - + +
137C ASP* 4.0 4.9 - - - +
139C ILE* 1.3 75.9 - - + +
141C LYS* 1.3 67.5 + - - +
143C ASP* 3.1 6.2 + - + +
144C GLN* 2.8 55.8 + - + +
216C VAL* 5.0 2.0 - - + -
217C LYS* 4.0 39.7 - - + +
220C LEU* 4.7 8.7 - - + -
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Residues in contact with LYS 141 (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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115C ILE 6.0 0.4 - - - -
116C GLU* 3.3 31.8 + - + +
118C LYS 4.8 7.0 + - - -
137C ASP 3.0 19.1 + - - +
138C VAL* 3.7 4.9 - - - +
140C VAL* 1.3 76.9 - - - +
142C VAL* 1.3 65.9 + - + +
144C GLN* 3.2 13.9 + - - +
145C ILE* 3.0 50.5 + - + +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE* 4.4 8.7 - - + +
123C PHE* 3.7 36.6 - - + -
129C VAL* 3.8 15.7 - - + -
131C LEU* 3.9 7.6 - - + -
138C VAL* 2.8 39.3 + - + +
141C LYS* 1.3 75.9 - - + +
143C ASP* 1.3 57.4 + - - +
145C ILE* 3.3 7.8 + - + +
146C CYS* 2.8 33.2 + - - -
153C PHE* 3.7 20.6 - - + -
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Residues in contact with ASP 143 (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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139C ILE 3.1 15.2 + - - +
140C VAL* 3.1 5.2 + - - +
142C VAL* 1.3 77.1 - - - +
144C GLN* 1.3 62.6 + - - +
146C CYS* 3.9 0.7 - - - +
147C HIS* 3.0 27.4 + - - +
153C PHE* 3.3 30.2 - - + +
168C ASN* 2.7 27.5 + - - +
215C PRO* 3.5 8.1 - - - +
216C VAL* 2.9 47.0 + - + +
217C LYS* 4.6 0.9 + - - +
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Residues in contact with GLN 144 (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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140C VAL* 2.8 41.4 + - + +
141C LYS* 3.6 11.4 - - - +
143C ASP* 1.3 79.0 - - - +
145C ILE* 1.3 67.5 + - + +
147C HIS* 3.4 5.3 + - - +
148C LYS* 3.0 26.0 + - - +
215C PRO* 6.0 3.8 - - + -
217C LYS* 4.1 17.6 - - + +
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Residues in contact with ILE 145 (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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118C LYS 5.1 1.6 - - - +
120C GLU* 3.6 39.9 - - + +
123C PHE* 4.0 39.5 - - + -
141C LYS* 3.0 49.0 + - + +
142C VAL* 3.7 6.7 - - + +
144C GLN* 1.3 78.5 - - + +
146C CYS* 1.3 60.4 - - - +
148C LYS* 3.6 7.5 + - + +
149C ASN* 3.0 33.8 + - - +
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Residues in contact with CYS 146 (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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123C PHE* 4.7 4.9 - - - -
129C VAL* 3.8 33.4 - - - -
142C VAL* 2.8 35.6 + - - +
143C ASP 3.9 3.4 - - - +
145C ILE* 1.3 75.9 - - - +
147C HIS* 1.3 59.4 + - - +
149C ASN 3.1 1.0 + - - -
150C SER 2.8 8.7 + - - -
151C ILE* 2.7 60.9 + - + +
153C PHE* 4.1 13.0 - - + -
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Residues in contact with HIS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ASP* 3.0 19.3 + - - +
144C GLN* 3.9 5.8 + - - +
146C CYS* 1.3 76.9 - - - +
148C LYS* 1.3 66.0 + - - +
150C SER* 3.1 15.0 + - - +
151C ILE 4.8 2.5 - - - -
153C PHE* 5.9 0.2 - - - +
168C ASN* 4.5 20.4 - - - +
170C GLY* 4.6 19.6 - - - -
213C PHE 5.9 1.8 + - - -
215C PRO* 5.2 15.9 - - + +
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Residues in contact with LYS 148 (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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120C GLU* 3.2 38.4 + - - +
144C GLN 3.0 18.7 + - - +
145C ILE* 3.7 7.4 - - - +
147C HIS* 1.3 83.2 + - - +
149C ASN* 1.3 59.1 + - - +
150C SER* 4.8 1.6 + - - -
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Residues in contact with ASN 149 (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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120C GLU* 3.4 37.1 + - - +
124C THR* 3.7 23.9 - - + +
145C ILE* 3.0 25.7 + - - +
146C CYS 3.1 2.2 + - - -
148C LYS* 1.3 80.3 - - - +
150C SER* 1.3 73.4 + - - +
151C ILE* 3.2 23.7 + - + +
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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