Contacts of the strand formed by residues 129 - 139 (chain C) in PDB entry 2HU4
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 CYS 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B ILE* 5.9 2.2 - - - -
100C TYR* 3.7 24.5 - - + +
122C ILE* 4.7 0.7 - - + -
123C SER 3.8 0.7 - - - -
124C CYS* 2.1 48.0 - - - -
128C GLU* 1.3 77.8 - - - +
130C ARG* 1.3 65.6 + - - +
162C PRO* 4.2 3.5 - - - +
163C VAL* 3.2 39.3 + - + +
412C LEU* 4.2 16.6 - - - -
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Residues in contact with ARG 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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122C ILE* 3.4 5.9 - - - +
123C SER 2.9 36.4 + - - +
128C GLU* 3.5 36.7 + - + -
129C CYS* 1.3 79.4 - - - +
131C THR* 1.3 65.1 + - - +
132C PHE* 4.1 13.2 - - + -
160C SER* 2.8 47.5 + - - -
161C CYS* 3.4 13.9 - - - +
162C PRO* 4.1 15.5 - - + +
163C VAL* 3.8 4.0 - - - +
170C ASN 5.2 0.8 + - - -
172C ARG* 3.7 39.4 - - - +
174C GLU* 4.6 0.2 + - - -
189C TRP* 4.2 19.1 - - + +
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Residues in contact with THR 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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103C ASP* 5.3 3.8 - - - +
120C PRO* 4.7 11.0 - - + -
121C PHE 3.4 8.3 - - - +
122C ILE* 4.1 7.9 - - + +
130C ARG* 1.3 71.4 - - - +
132C PHE* 1.3 73.1 + - - +
133C PHE* 3.6 14.1 - - + -
160C SER* 3.1 5.5 - - - -
161C CYS* 2.9 41.2 + - - -
162C PRO 4.8 0.2 - - - -
163C VAL* 3.3 28.1 - - - +
164C GLY 4.2 3.5 + - - -
165C GLU 5.8 1.3 - - - +
167C PRO* 6.4 1.6 - - + -
443C SER* 4.8 13.0 + - - +
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Residues in contact with PHE 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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120C PRO* 3.2 1.2 - - - +
121C PHE* 2.6 73.2 + + + -
123C SER* 3.9 22.0 - - - -
130C ARG* 4.1 17.5 - - + -
131C THR* 1.3 77.4 - - - +
133C PHE* 1.3 65.8 + - - +
158C LEU* 4.1 8.3 - - + -
159C MET 3.4 6.5 - - - +
160C SER* 3.6 23.1 - - - -
172C ARG* 5.8 0.2 - - - -
174C GLU* 3.7 22.9 - - + -
182C ALA* 4.1 15.9 - - + -
189C TRP* 3.9 35.0 - + - -
191C THR* 4.4 5.2 - - + -
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Residues in contact with PHE 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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115C PHE* 4.5 2.7 - + - -
117C ILE* 3.6 39.9 - - + -
119C GLU 3.6 9.4 - - - -
120C PRO* 3.9 5.8 - - + -
121C PHE* 5.4 0.2 - - - -
131C THR* 3.6 25.4 - - + -
132C PHE* 1.3 82.1 - - - +
134C LEU* 1.3 63.6 + - - +
135C THR* 3.5 22.9 - - + -
157C THR 3.5 0.7 - - - +
158C LEU* 3.5 6.7 - - - +
159C MET* 3.1 45.0 + - + -
160C SER* 3.8 8.7 - - - -
161C CYS* 3.9 10.3 - - - -
167C PRO* 3.4 31.2 - - + -
171C SER* 3.6 17.5 - - - -
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Residues in contact with LEU 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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117C ILE* 3.3 4.2 - - - -
118C ARG 3.2 32.2 + - - +
119C GLU* 3.7 34.5 - - + +
121C PHE* 6.2 1.1 - - + -
133C PHE* 1.3 73.2 - - - +
135C THR* 1.3 64.1 + - - +
156C ARG* 3.4 13.9 + - + +
157C THR 3.6 0.9 - - - -
158C LEU* 3.8 33.2 - - + -
177C ALA 3.8 18.8 - - - +
178C TRP* 3.7 25.4 - - - +
179C SER 3.7 1.1 - - - +
180C ALA* 3.9 9.9 - - + -
227C GLU* 3.7 16.2 - - - +
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Residues in contact with THR 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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115C PHE* 4.1 20.0 - - + -
116C VAL 3.4 10.1 - - - -
117C ILE* 4.0 2.0 - - + -
133C PHE* 3.5 29.2 - - + -
134C LEU* 1.3 72.0 - - - +
136C GLN* 1.3 60.9 + - - +
137C GLY* 3.4 11.1 + - - -
156C ARG* 2.9 29.6 + - - +
157C THR* 2.7 36.8 + - - +
159C MET* 4.0 18.3 - - + -
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Residues in contact with GLN 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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107A ARG* 2.7 32.1 + - - -
116C VAL* 3.1 40.8 + - + +
117C ILE* 5.0 1.6 - - - -
118C ARG* 5.3 2.4 - - + +
134C LEU 4.9 0.4 - - - +
135C THR* 1.3 74.3 - - - +
137C GLY* 1.3 55.2 + - - +
138C ALA* 3.0 2.7 + - - +
148C THR* 3.3 38.5 + - + +
150C LYS* 4.5 11.4 - - - +
151C ASP* 4.5 9.9 - - - +
153C SER* 4.3 8.3 + - - -
155C HIS* 4.2 7.4 - - - +
156C ARG* 2.9 52.4 - - - +
439C THR 5.2 0.4 - - - +
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Residues in contact with GLY 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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104A ASN* 3.6 30.4 - - - +
107A ARG* 2.7 35.9 + - - +
108A ILE* 4.1 10.6 - - - +
115C PHE* 5.1 1.6 - - - -
135C THR* 3.4 13.9 + - - -
136C GLN* 1.3 78.1 - - - +
138C ALA* 1.3 55.9 + - - +
155C HIS 3.7 4.0 + - - -
157C THR* 5.5 0.2 - - - -
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Residues in contact with ALA 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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107A ARG* 3.9 3.1 - - - +
108A ILE* 4.6 5.5 - - - +
115C PHE* 3.7 11.4 - - - -
116C VAL* 2.9 33.9 + - + +
136C GLN* 3.0 9.1 + - + +
137C GLY* 1.3 79.6 - - - +
139C LEU* 1.3 64.8 + - - +
144C HIS* 3.3 42.2 - - + +
145C SER* 4.1 1.3 - - - +
148C THR* 5.1 0.2 - - + -
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Residues in contact with LEU 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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108A ILE* 3.5 31.9 - - + +
111A LYS* 4.0 11.7 - - + -
112A GLY* 3.4 35.9 - - - +
113C ASP* 3.9 16.8 - - + +
114C VAL 3.4 24.0 - - - +
115C PHE* 4.0 12.1 - - + +
116C VAL* 4.5 3.8 - - - -
138C ALA* 1.3 83.6 - - - +
140C LEU* 1.3 68.6 + - - +
142C ASP* 3.5 16.3 + - + +
145C SER* 3.4 19.9 - - - -
169C PRO* 4.2 11.4 - - + -
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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