Contacts of the strand formed by residues 157 - 163 (chain E) in PDB entry 3T0E
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 TRP 157 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E LEU* 5.8 0.9 - - + -
116E LEU* 6.1 1.8 - - + -
130E CYS* 3.7 33.7 - - + -
131E ARG 3.6 4.9 - - - -
132E SER* 3.9 29.2 - - - -
133E PRO* 3.4 9.4 - - + +
136E LYS* 5.2 2.0 - - + -
138E ILE* 4.2 14.1 - - + -
146E VAL* 3.9 34.5 - - + -
149E LEU* 5.1 4.9 - - + +
153E ASP* 3.2 36.9 + - + -
155E GLY 3.1 24.7 + - - -
156E THR* 1.3 77.3 - - - +
158E THR* 1.3 71.5 + - - +
171E LYS* 3.6 17.5 - - - -
172E ILE* 3.0 30.4 + - + +
174E ILE* 3.5 28.7 - - + +
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Residues in contact with THR 158 (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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129E GLN 3.8 0.2 - - - +
130E CYS* 3.2 4.4 - - - -
131E ARG* 2.9 61.1 + - - +
156E THR* 4.8 4.9 - - + +
157E TRP* 1.3 84.0 - - - +
159E CYS* 1.3 64.4 + - - +
160E THR* 4.1 4.6 + - - -
169E GLU* 6.4 0.7 - - - -
170E PHE 3.3 7.0 - - - -
171E LYS* 3.1 33.7 - - + +
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Residues in contact with CYS 159 (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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100E LEU* 3.4 25.1 - - + -
116E LEU* 3.6 24.0 - - - -
128E VAL* 4.7 4.9 - - + -
129E GLN 3.2 2.5 - - - +
130E CYS* 2.0 44.4 - - - -
144E LEU* 4.9 0.2 - - - -
157E TRP 4.4 0.2 - - - -
158E THR* 1.3 73.9 - - - +
160E THR* 1.3 63.1 + - - +
161E VAL 4.1 0.2 - - - -
168E VAL 3.4 5.4 - - - +
169E GLU* 4.3 0.9 - - - -
170E PHE* 2.7 41.9 + - + +
172E ILE* 4.3 8.3 - - + +
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Residues in contact with THR 160 (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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127E SER 3.9 0.2 - - - +
128E VAL* 3.2 6.9 - - - -
129E GLN* 2.8 53.5 + - + +
158E THR* 4.7 4.9 + - - -
159E CYS* 1.3 74.6 + - - +
161E VAL* 1.3 70.6 + - - +
162E LEU* 4.1 5.6 + - + +
167E LYS* 3.7 33.7 - - + -
168E VAL 3.9 6.5 + - - +
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Residues in contact with VAL 161 (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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98E PHE* 4.1 21.5 - - + -
100E LEU* 5.2 3.4 - - + -
118E LEU* 4.0 24.5 - - + -
126E PRO* 3.6 24.0 - - + -
127E SER 3.3 16.2 - - - +
128E VAL* 4.7 9.6 - - + -
159E CYS 4.1 0.2 + - - -
160E THR* 1.3 80.1 - - - +
162E LEU* 1.3 65.4 + - - +
163E GLN 4.2 0.2 - - - -
166E LYS 4.0 3.5 - - - +
167E LYS* 4.2 1.0 - - - -
168E VAL* 3.2 44.0 + - + +
170E PHE* 4.5 15.0 - - + -
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Residues in contact with LEU 162 (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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125E SER 4.9 1.0 - - - +
126E PRO* 4.0 16.5 - - - +
127E SER* 3.5 18.3 + - - +
160E THR* 4.1 6.0 + - + +
161E VAL* 1.3 80.1 - - - +
163E GLN* 1.3 71.8 + - - +
165E GLN* 4.0 18.4 - - - +
166E LYS 3.6 30.5 - - - +
167E LYS* 4.4 23.8 - - + +
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Residues in contact with GLN 163 (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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5E LEU* 4.6 17.0 - - + +
96E LEU* 4.9 9.2 - - + -
98E PHE* 4.4 24.5 - - + -
124E SER* 4.5 6.2 - - - -
125E SER* 3.5 46.0 + - - -
126E PRO* 3.6 6.9 - - + +
161E VAL 4.2 0.6 - - - -
162E LEU* 1.3 78.0 + - - +
164E ASN* 1.3 91.0 + - + +
165E GLN 2.9 3.2 + - - -
166E LYS* 3.0 20.2 + - - +
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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