Contacts of the strand formed by residues 129 - 139 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E TYR* 3.7 27.6 - - + +
122E ILE* 4.4 1.8 - - + -
123E SER 3.9 1.1 - - - -
124E CYS* 2.1 47.8 - - - -
128E GLU* 1.3 80.1 - - - +
130E ARG* 1.3 65.5 + - - +
162E PRO* 4.0 5.0 - - - +
163E VAL* 3.6 33.8 + - + +
410E PHE* 4.8 0.4 - - - -
412E LEU* 4.3 14.4 - - - -
210G ILE* 5.8 2.0 - - - -
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Residues in contact with ARG 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E ILE* 3.3 6.6 - - - +
123E SER 3.1 33.7 + - - +
128E GLU* 3.4 36.6 + - + +
129E CYS* 1.3 80.1 - - - +
131E THR* 1.3 62.9 + - - +
132E PHE* 4.0 14.4 + - + -
160E SER* 2.9 50.3 + - - +
161E CYS* 3.3 14.8 - - - +
162E PRO* 4.3 13.1 - - + +
163E VAL* 3.8 2.7 - - - -
170E ASN 5.1 1.2 + - - -
172E ARG* 3.3 41.7 - - - +
189E TRP* 4.0 18.2 - - + +
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Residues in contact with THR 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ASP* 5.2 5.1 + - - +
120E PRO* 4.7 7.9 - - + -
121E PHE 3.7 12.1 - - - +
122E ILE* 4.0 9.9 - - + +
130E ARG* 1.3 72.7 - - - +
132E PHE* 1.3 70.0 + - - +
133E PHE* 3.3 14.9 - - + -
160E SER* 3.2 5.3 - - - -
161E CYS* 2.7 41.9 + - - -
163E VAL* 3.2 29.7 - - - +
164E GLY 4.3 1.9 + - - -
165E GLU 5.9 1.3 - - - +
443E SER* 4.8 12.5 + - - +
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Residues in contact with PHE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E PRO* 3.3 0.9 - - - +
121E PHE* 2.8 73.1 + + + +
123E SER* 4.0 8.1 - - - -
130E ARG* 4.3 15.7 - - + -
131E THR* 1.3 77.3 - - - +
133E PHE* 1.3 65.0 + - - +
158E LEU* 4.0 10.3 - - + -
159E MET 3.4 4.9 - - - -
160E SER* 3.7 20.2 - - - -
172E ARG* 5.3 0.4 - - - -
174E GLU* 4.0 26.5 - - + -
182E ALA* 3.8 18.4 - - + -
189E TRP* 3.5 52.5 - + - -
191E THR* 4.4 4.3 - - + -
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Residues in contact with PHE 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E PHE* 4.3 2.5 - + - -
117E ILE* 3.9 31.9 - - + -
118E ARG 4.5 0.2 - - - +
119E GLU 3.9 8.5 - - - -
120E PRO* 4.1 5.4 - - + -
131E THR* 3.3 28.9 - - + -
132E PHE* 1.3 77.5 - - - +
134E LEU* 1.3 62.4 + - - +
135E THR* 3.5 22.9 - - + -
158E LEU* 3.3 8.3 - - - +
159E MET* 2.9 57.5 + - + -
160E SER* 3.6 5.8 - - - -
161E CYS* 3.7 10.1 - - - -
167E PRO* 3.5 24.5 - - + -
171E SER* 3.4 24.2 - - - -
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Residues in contact with LEU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ILE* 3.4 2.6 - - - -
118E ARG 3.2 33.8 + - - +
119E GLU* 3.7 30.9 + - + +
121E PHE* 6.2 1.1 - - + -
133E PHE* 1.3 74.4 - - - +
135E THR* 1.3 65.4 + - - +
156E ARG* 3.2 16.0 + - + +
157E THR 3.6 1.1 - - - -
158E LEU* 3.9 27.6 - - + +
177E ALA 3.6 24.0 - - - +
178E TRP 3.8 24.9 - - - +
179E SER* 3.8 2.5 - - - +
180E ALA* 4.2 13.2 - - + +
227E GLU* 3.9 12.1 - - - +
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Residues in contact with THR 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E PHE* 3.7 29.6 - - + -
116E VAL 3.4 11.0 - - - -
117E ILE* 4.0 1.1 - - - -
133E PHE* 3.5 31.0 - - + -
134E LEU* 1.3 73.6 - - - +
136E GLN* 1.3 57.9 + - - +
137E GLY* 3.5 10.9 + - - -
156E ARG* 2.7 34.5 + - - +
157E THR* 2.7 33.9 + - - +
159E MET* 4.2 10.4 - - - -
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Residues in contact with GLN 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E VAL* 3.2 27.5 + - + +
117E ILE* 4.8 1.6 - - - -
118E ARG* 5.1 4.2 - - - +
135E THR* 1.3 74.3 - - - +
137E GLY* 1.3 53.8 + - - +
138E ALA* 3.1 2.3 + - - +
148E THR* 3.3 50.7 + - + +
150E LYS* 4.5 10.7 - - - +
151E ASP* 4.6 8.3 + - - +
153E SER* 4.2 8.2 + - - -
155E HIS* 4.1 8.5 - - - +
156E ARG* 2.8 54.3 - - - +
107H ARG* 2.6 33.1 + - - -
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Residues in contact with GLY 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E PHE* 5.5 1.6 - - - -
135E THR* 3.5 11.5 + - - -
136E GLN* 1.3 79.3 - - - +
138E ALA* 1.3 56.3 + - - +
155E HIS 3.7 2.7 + - - -
104H ASN* 3.4 30.5 - - - +
107H ARG* 2.8 36.9 + - - +
108H ILE* 4.1 10.8 - - - +
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Residues in contact with ALA 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E PHE* 3.5 10.2 - - - -
116E VAL* 2.8 36.3 + - + +
136E GLN* 3.1 5.6 - - + +
137E GLY* 1.3 81.9 - - - +
139E LEU* 1.3 67.7 + - - +
142E ASP* 5.0 0.2 - - - +
144E HIS* 3.4 42.2 - - + +
145E SER* 4.1 1.8 - - - +
107H ARG* 4.1 3.6 - - - +
108H ILE* 4.7 4.8 - - - +
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ASP* 3.9 21.1 - - + +
114E VAL 3.4 18.6 - - - +
115E PHE* 3.8 22.9 - - + +
116E VAL* 4.4 4.3 - - - -
138E ALA* 1.3 83.6 - - - +
140E LEU* 1.3 71.1 + - - +
142E ASP* 3.4 22.4 + - + +
145E SER* 3.5 10.7 - - - -
169E PRO* 4.1 13.0 - - + -
107H ARG 5.3 1.4 + - - +
108H ILE* 3.8 22.7 - - + +
111H LYS* 4.3 9.0 - - + -
112H GLY* 3.7 33.9 - - - +
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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