Contacts of the strand formed by residues 129 - 139 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ILE* 5.8 1.8 - - - -
100D TYR* 3.9 23.3 - - + +
122D ILE* 4.4 1.3 - - + -
123D SER 3.7 3.6 - - - +
124D CYS* 2.1 44.2 - - - -
128D GLU* 1.3 78.3 - - - +
130D ARG* 1.3 64.4 + - - +
162D PRO* 3.8 4.5 - - - +
163D VAL* 3.3 41.0 + - + +
410D PHE* 5.0 0.4 - - - -
412D LEU* 4.4 13.9 - - - -
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Residues in contact with ARG 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PHE 4.0 0.2 - - - +
122D ILE* 3.3 5.9 - - - +
123D SER 3.0 31.4 + - - +
128D GLU* 3.4 35.0 + - - +
129D CYS* 1.3 79.5 - - - +
131D THR* 1.3 61.9 + - - +
132D PHE* 4.0 15.9 + - + -
160D SER* 2.9 49.3 + - - -
161D CYS* 3.5 15.1 - - - +
162D PRO* 4.1 14.9 - - + +
163D VAL* 3.9 2.7 - - - +
170D ASN 5.1 1.2 + - - -
172D ARG* 3.6 35.0 - - - +
189D TRP* 4.0 27.4 - - + +
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Residues in contact with THR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASP* 5.0 4.4 + - - +
120D PRO* 4.7 6.3 - - + -
121D PHE 3.5 12.6 - - - +
122D ILE* 4.0 9.0 - - + +
130D ARG* 1.3 71.2 - - - +
132D PHE* 1.3 72.5 + - - +
133D PHE* 3.5 12.1 - - + -
160D SER* 3.1 3.5 - - - -
161D CYS* 2.7 43.4 + - - -
162D PRO 4.0 0.3 + - - -
163D VAL* 3.3 28.1 - - - +
164D GLY 4.2 3.1 + - - -
165D GLU 5.4 1.3 + - - +
167D PRO* 6.5 0.7 - - + -
443D SER* 4.5 17.2 + - - +
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PRO* 3.3 1.4 - - - +
121D PHE* 2.7 67.0 + + + -
123D SER* 3.8 22.4 - - - -
130D ARG* 4.1 16.2 - - + -
131D THR* 1.3 78.2 - - - +
133D PHE* 1.3 67.4 + - - +
158D LEU* 4.1 10.1 - - + -
159D MET 3.2 8.3 - - - +
160D SER* 3.7 13.5 - - - -
174D GLU* 3.8 29.6 - - + -
182D ALA* 3.8 18.6 - - + -
189D TRP* 3.6 37.0 - + - -
191D THR* 4.5 5.2 - - + -
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Residues in contact with PHE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D PHE* 4.3 4.3 - + - -
117D ILE* 3.7 31.9 - - + -
118D ARG 4.4 0.7 - - - +
119D GLU 3.9 9.2 - - - -
120D PRO* 4.1 10.3 - - + -
131D THR* 3.5 23.6 - - + -
132D PHE* 1.3 81.9 - - - +
134D LEU* 1.3 59.8 + - - +
135D THR* 3.6 22.0 - - + -
157D THR 3.5 0.3 - - - +
158D LEU* 3.3 10.8 - - - +
159D MET* 2.9 38.1 + - + -
160D SER* 3.7 16.6 - - - -
161D CYS* 3.8 9.4 - - - -
167D PRO* 3.3 31.9 - - + -
171D SER* 3.5 17.5 - - - -
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ILE* 3.6 2.6 - - - -
118D ARG 3.3 22.4 + - - +
119D GLU* 3.6 34.5 - - + +
121D PHE* 6.4 0.7 - - + -
133D PHE* 1.3 74.1 - - - +
135D THR* 1.3 61.7 + - - +
156D ARG* 3.0 29.5 + - + +
157D THR 3.4 2.2 - - - +
158D LEU* 4.0 30.3 - - + -
177D ALA 3.8 18.8 - - - +
178D TRP* 3.6 26.7 - - - +
179D SER* 3.7 9.9 - - - +
180D ALA* 4.0 12.6 - - + +
227D GLU* 4.3 3.8 - - - +
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Residues in contact with THR 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D PHE* 3.7 28.3 - - + -
116D VAL 3.4 11.4 - - - -
117D ILE* 4.0 1.1 - - - -
133D PHE* 3.6 28.9 - - + -
134D LEU* 1.3 73.8 - - - +
136D GLN* 1.3 60.1 + - - +
137D GLY* 3.3 13.1 + - - -
156D ARG* 3.0 28.5 + - - +
157D THR* 2.7 33.1 + - - +
159D MET* 4.0 13.1 - - - -
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 2.9 19.4 + - - -
116D VAL* 3.1 25.9 + - + +
117D ILE* 5.1 1.1 - - - +
118D ARG* 5.6 1.4 - - + +
135D THR* 1.3 73.1 - - - +
137D GLY* 1.3 65.2 + - - +
138D ALA* 3.1 2.0 + - - +
148D THR* 3.4 55.4 + - + +
150D LYS* 4.5 10.1 - - - +
151D ASP* 4.5 10.3 - - - +
153D SER* 4.0 9.0 + - - -
155D HIS* 4.0 8.8 - - - +
156D ARG* 2.9 50.3 - - - +
439D THR 5.2 0.7 - - - +
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Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ASN* 3.6 28.9 - - - +
107B ARG* 2.9 35.0 + - - +
108B ILE* 4.1 9.1 - - - +
115D PHE* 5.2 2.9 - - - -
135D THR* 3.3 13.8 + - - -
136D GLN* 1.3 78.3 - - - +
138D ALA* 1.3 54.6 + - - +
155D HIS 3.6 6.3 + - - -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 3.9 2.2 - - - +
108B ILE* 4.6 7.3 - - - +
115D PHE* 3.5 13.2 - - - -
116D VAL* 3.0 35.0 + - + +
136D GLN* 3.1 6.6 - - + +
137D GLY* 1.3 80.1 - - - +
139D LEU* 1.3 64.8 + - - +
144D HIS* 3.5 42.8 - - + +
145D SER* 4.2 1.1 - - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 3.5 26.4 - - + +
111B LYS* 4.0 13.9 - - + -
112B GLY* 3.5 35.2 - - - +
113D ASP* 4.0 15.7 - - + -
114D VAL 3.4 24.5 - - - +
115D PHE* 4.0 8.1 - - + +
116D VAL* 4.5 4.7 - - - -
138D ALA* 1.3 81.7 - - - +
140D LEU* 1.3 70.5 + - - +
141D ASN 3.6 0.2 + - - -
142D ASP* 3.5 20.4 + - + +
145D SER* 3.6 11.3 - - - -
169D PRO* 3.8 22.4 - - + -
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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