Contacts of the strand formed by residues 129 - 139 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210F ILE* 5.7 1.6 - - - -
100G TYR* 4.0 21.8 - - + +
122G ILE* 4.6 1.8 - - + -
123G SER 3.7 0.4 - - - -
124G CYS* 2.1 46.9 - - - -
128G GLU* 1.3 78.0 - - - +
130G ARG* 1.3 65.7 + - - +
162G PRO* 4.0 5.5 - - - +
163G VAL* 3.6 37.8 + - + +
410G PHE* 4.9 0.2 - - - -
412G LEU* 4.2 17.0 - - - -
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Residues in contact with ARG 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G PHE 4.1 0.2 - - - +
122G ILE* 3.2 8.3 - - - +
123G SER 2.9 33.8 + - - +
128G GLU* 3.4 33.5 + - + +
129G CYS* 1.3 79.3 - - - +
131G THR* 1.3 65.9 + - - +
132G PHE* 4.1 12.7 + - + -
160G SER* 2.7 45.8 + - - -
161G CYS* 3.5 12.9 - - - +
162G PRO* 3.9 18.1 - - + +
163G VAL* 3.7 2.7 - - - +
170G ASN 5.4 0.8 + - - -
172G ARG* 3.4 41.0 - - - +
174G GLU* 4.7 0.2 + - - -
189G TRP* 3.9 23.3 - - + -
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Residues in contact with THR 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ASP* 5.4 3.1 - - - +
120G PRO* 4.6 7.9 - - + -
121G PHE 3.4 14.1 - - - +
122G ILE* 4.2 8.1 - - + +
130G ARG* 1.3 72.0 - - - +
132G PHE* 1.3 75.8 + - - +
133G PHE* 3.5 11.0 - - + -
160G SER* 3.1 4.6 - - - -
161G CYS* 2.8 42.3 + - - -
162G PRO 4.2 0.2 + - - -
163G VAL* 3.2 30.2 - - - +
164G GLY 4.3 2.3 + - - -
165G GLU 5.7 0.8 + - - -
443G SER* 4.8 12.3 - - - +
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Residues in contact with PHE 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G PRO* 3.3 1.0 - - - +
121G PHE* 2.8 68.2 + + + +
123G SER* 3.9 11.7 - - - -
130G ARG* 4.3 14.6 - - + -
131G THR* 1.3 80.3 - - - +
133G PHE* 1.3 67.4 + - - +
158G LEU* 4.0 10.1 - - + -
159G MET 3.4 5.4 - - - -
160G SER* 3.7 13.9 - - - -
172G ARG* 5.7 0.4 - - - -
174G GLU* 3.6 33.0 - - + -
182G ALA* 3.8 19.1 - - + -
189G TRP* 3.5 50.0 - + - -
191G THR* 4.5 3.6 - - + -
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Residues in contact with PHE 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G PHE* 4.4 2.9 - + - -
117G ILE* 3.6 39.3 - - + -
118G ARG 4.4 0.2 - - - +
119G GLU 3.7 10.8 - - - -
120G PRO* 4.0 4.7 - - + -
121G PHE* 4.9 0.9 - - - -
131G THR* 3.5 19.5 - - + -
132G PHE* 1.3 83.4 - - - +
134G LEU* 1.3 62.6 + - - +
135G THR* 3.4 25.6 - - + -
158G LEU* 3.4 7.7 - - - +
159G MET* 3.0 51.5 + - + -
160G SER* 3.9 4.9 - - - -
161G CYS* 3.9 9.4 - - - -
167G PRO* 3.4 33.9 - - + -
171G SER* 3.5 16.4 - - - -
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ILE* 3.5 2.8 - - - -
118G ARG 3.2 32.0 + - - +
119G GLU* 3.4 36.3 - - + +
121G PHE* 6.2 0.9 - - + -
133G PHE* 1.3 75.5 - - - +
135G THR* 1.3 65.8 + - - +
156G ARG* 3.5 12.9 + - - +
157G THR 3.6 2.0 - - - -
158G LEU* 4.0 15.5 - - + -
177G ALA 3.5 24.5 - - - +
178G TRP 3.8 22.4 - - - +
179G SER* 3.9 0.9 - - - +
180G ALA* 3.8 25.4 - - + +
227G GLU* 3.9 13.7 - - - +
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Residues in contact with THR 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G PHE* 3.8 26.6 - - + -
116G VAL 3.5 11.4 - - - -
117G ILE* 4.0 1.1 - - - -
133G PHE* 3.4 30.3 - - + -
134G LEU* 1.3 73.8 - - - +
136G GLN* 1.3 60.7 + - - +
137G GLY* 3.3 13.7 + - - -
156G ARG* 2.9 29.7 + - - +
157G THR* 2.8 32.6 + - - +
159G MET* 4.0 12.5 - - - -
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Residues in contact with GLN 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ARG* 2.7 31.4 + - - -
116G VAL* 3.2 25.3 + - + +
117G ILE* 5.1 2.5 - - - -
118G ARG* 5.2 3.4 - - + +
134G LEU 4.9 0.2 - - - +
135G THR* 1.3 73.2 - - - +
137G GLY* 1.3 54.9 + - - +
138G ALA* 3.0 2.5 + - - +
148G THR* 2.8 59.6 + - + +
150G LYS* 4.7 9.2 - - - +
151G ASP* 4.6 8.9 - - - +
153G SER* 4.2 8.0 + - - -
155G HIS* 4.0 8.0 - - - +
156G ARG* 3.1 49.6 - - - +
439G THR 5.3 0.2 - - - +
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Residues in contact with GLY 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ASN* 3.6 27.6 - - - +
107E ARG* 2.8 35.8 + - - +
108E ILE* 4.2 10.5 - - - +
115G PHE* 5.1 1.3 - - - -
135G THR* 3.3 14.4 + - - -
136G GLN* 1.3 78.3 - - - +
138G ALA* 1.3 55.9 + - - +
155G HIS 3.5 5.7 + - - -
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Residues in contact with ALA 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ARG* 4.0 5.4 - - - +
108E ILE* 4.6 4.9 - - - -
115G PHE* 3.4 16.1 - - - -
116G VAL* 3.2 32.1 + - + +
136G GLN* 3.0 9.9 + - + +
137G GLY* 1.3 79.8 - - - +
139G LEU* 1.3 64.8 + - - +
144G HIS* 3.6 37.9 - - + +
145G SER* 4.1 0.9 - - - +
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Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ARG 5.3 1.4 + - - -
108E ILE* 3.5 26.2 - - + +
111E LYS* 4.0 13.9 - - + +
112E GLY* 3.5 34.8 - - - +
113G ASP* 4.0 15.5 - - + +
114G VAL 3.4 18.4 - - - +
115G PHE* 4.1 5.8 - - + +
116G VAL* 4.5 2.7 - - - -
138G ALA* 1.3 84.5 - - - +
140G LEU* 1.3 72.6 + - - +
142G ASP* 3.3 21.3 + - + +
145G SER* 3.5 11.0 - - - -
169G PRO* 3.9 25.8 - - + -
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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