Contacts of the helix formed by residues 127 - 139 (chain C) in PDB entry 2YMB
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 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C ARG* 1.3 94.3 - - + +
128C THR* 1.3 66.9 + - - +
129C HIS* 3.5 23.6 - + + +
130C GLN* 3.0 20.0 + - - +
131C LEU* 3.1 19.7 + - - +
158C ASP* 4.5 3.6 - - - -
162C GLU* 3.9 29.1 + - - -
165C GLN* 5.2 1.6 - - - +
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Residues in contact with THR 128 (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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221A PHE* 5.1 5.6 - - + -
127C HIS* 1.3 74.9 - - - +
129C HIS* 1.3 63.7 + - - +
131C LEU* 3.1 23.0 + - - +
132C TYR* 3.1 34.9 + - + -
165C GLN* 4.0 18.8 + - - +
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Residues in contact with HIS 129 (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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127C HIS* 3.8 23.0 - + + +
128C THR* 1.3 80.5 + - - +
130C GLN* 1.3 77.3 + - + +
132C TYR* 3.4 9.1 + - - +
133C ASN* 2.9 36.5 + - - +
212C ASP* 3.4 31.1 + - - -
214C PHE* 5.6 3.4 - - + -
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Residues in contact with GLN 130 (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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124C TYR* 3.3 38.2 + - - +
125C ILE* 3.9 13.7 - - + +
126C ARG* 2.6 34.5 + - - +
127C HIS* 3.0 24.0 + - - +
128C THR 3.2 0.4 - - - -
129C HIS* 1.3 99.7 - - + +
131C LEU* 1.3 63.5 + - - +
133C ASN* 3.3 10.2 + - - +
134C PHE* 3.1 22.2 + - - +
212C ASP* 3.3 25.6 + - + +
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Residues in contact with LEU 131 (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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221A PHE* 3.8 21.5 - - + -
125C ILE* 3.8 22.9 - - + +
126C ARG 4.1 7.9 - - - +
127C HIS 3.1 14.9 + - - +
128C THR* 3.1 13.8 + - - +
130C GLN* 1.3 77.7 - - - +
132C TYR* 1.3 56.2 + - - +
134C PHE* 3.3 5.0 + - - +
135C LEU* 3.0 26.0 + - - +
165C GLN* 3.7 25.8 - - + +
166C GLN* 4.6 2.9 - - - +
169C GLY* 3.8 13.2 - - - -
170C LEU* 3.7 35.4 - - + +
173C ILE* 3.7 9.8 - - + +
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Residues in contact with TYR 132 (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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220A ARG* 3.0 28.6 + - - +
221A PHE* 3.4 24.0 - + - -
225A TYR* 3.6 43.4 + + - -
226A CYS* 4.3 10.5 - - - -
128C THR* 3.1 40.3 + - + -
129C HIS* 3.4 10.7 + - - +
130C GLN 3.3 0.2 - - - -
131C LEU* 1.3 73.8 - - - +
133C ASN* 1.3 66.2 + - - +
135C LEU* 3.4 16.7 - - + +
136C ARG* 3.0 38.7 + - - +
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Residues in contact with ASN 133 (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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103C TYR* 3.1 31.5 - - - +
125C ILE* 6.1 0.4 - - + -
129C HIS* 2.9 25.1 + - - +
130C GLN* 3.3 15.4 - - - +
132C TYR* 1.3 77.5 - - - +
134C PHE* 1.3 62.0 + - - +
136C ARG* 2.6 35.3 + - - +
137C PHE* 3.0 18.8 + - - +
211C LEU* 3.7 19.5 + - + +
212C ASP* 3.8 21.2 + - - +
214C PHE* 4.1 9.6 - - - +
228C PHE* 4.5 2.1 - - - -
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Residues in contact with PHE 134 (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 ILE* 4.1 14.4 - - + -
125C ILE* 4.2 18.4 - - + -
130C GLN 3.1 10.1 + - - +
131C LEU* 3.5 7.0 - - - +
133C ASN* 1.3 79.5 - - - +
135C LEU* 1.3 57.8 + - - +
137C PHE* 3.3 17.4 - + - +
138C CYS* 2.9 54.2 + - - -
151C ILE* 4.5 4.0 - - + -
153C LEU* 3.9 39.7 - - + -
170C LEU* 4.3 9.0 - - + -
173C ILE* 4.0 27.8 - - + -
184C LEU* 4.0 24.9 - - + -
211C LEU* 4.5 11.6 - - + +
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Residues in contact with LEU 135 (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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220A ARG 4.6 0.7 - - - +
221A PHE* 3.7 51.1 - - + +
222A SER 4.3 3.8 - - - +
223A LEU* 4.2 23.8 - - + -
225A TYR* 4.6 4.9 - - + -
226A CYS* 5.6 2.0 - - - -
131C LEU 3.0 12.8 + - - +
132C TYR* 3.4 24.2 - - + +
133C ASN 3.2 0.4 - - - -
134C PHE* 1.3 74.2 - - - +
136C ARG* 1.3 61.0 + - + +
138C CYS* 3.0 9.3 + - + +
139C GLU* 2.9 43.7 + - + +
173C ILE* 4.1 15.9 - - + -
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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
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226A CYS* 3.7 37.2 - - + -
103C TYR* 3.6 17.9 - - + +
129C HIS 4.7 0.2 + - - -
132C TYR* 3.0 36.6 + - - +
133C ASN* 2.6 38.9 + - - +
135C LEU* 1.3 75.7 - - - +
137C PHE* 1.3 61.5 + - - +
139C GLU* 3.4 29.7 + - - +
140C MET* 4.3 4.0 - - - +
214C PHE* 3.5 27.3 - - - -
226C CYS 5.1 1.6 - - - -
228C PHE* 3.3 44.1 - - - +
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Residues in contact with PHE 137 (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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103C TYR* 3.8 16.1 - + + -
107C PHE* 3.9 35.7 - + - -
118C VAL* 4.5 18.2 - - + -
120C ILE* 4.8 14.8 - - + -
133C ASN 3.0 15.0 + - - +
134C PHE* 3.3 28.3 - + - +
136C ARG* 1.3 77.6 - - - +
138C CYS* 1.3 67.1 + - - +
140C MET* 3.3 29.9 - - + +
151C ILE* 5.6 5.8 - - + -
197C ILE* 4.1 27.1 - - + -
199C PHE* 4.7 5.6 - + - -
211C LEU* 4.2 20.6 - - + -
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Residues in contact with CYS 138 (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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223A LEU* 4.4 4.4 - - + +
134C PHE* 2.9 55.3 + - - +
135C LEU* 3.0 12.1 + - + +
137C PHE* 1.3 76.3 - - - +
139C GLU* 1.3 50.9 + - - +
140C MET* 2.5 24.3 + - - +
141C LEU* 3.3 17.3 - - - +
151C ILE* 4.3 16.9 - - + +
173C ILE* 4.6 3.4 - - + -
177C LEU* 3.7 33.7 - - + +
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Residues in contact with GLU 139 (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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223A LEU* 4.1 6.4 - - + -
224A GLY 3.1 21.8 + - - +
225A TYR 3.6 0.9 + - - -
226A CYS* 3.3 15.7 + - - +
227A ASP* 3.2 49.2 + - + +
230A LEU* 4.3 15.0 - - + -
135C LEU* 2.9 27.1 + - + +
136C ARG* 3.4 32.9 - - - +
137C PHE 3.2 0.6 - - - -
138C CYS* 1.3 70.7 - - - +
140C MET* 1.3 64.9 + - - +
141C LEU* 4.0 7.9 - - - -
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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