Contacts of the strand formed by residues 132 - 139 (chain X) in PDB entry 4LAH
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 132 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X ILE* 3.9 14.5 - - + +
106X VAL* 4.1 5.8 - - + -
107X ASP 3.9 8.1 - - - -
108X ASP* 3.9 4.0 - - - -
109X MET* 3.5 41.8 - - + +
127X TYR* 4.1 19.7 - + + +
128X THR 3.1 26.7 - - - +
129X PHE* 3.0 30.3 + - + +
131X ASP* 1.3 93.4 + - + +
133X GLU* 1.3 61.3 + - - +
134X VAL* 3.8 1.7 + - - +
155X LEU* 3.9 29.2 - - + -
156X ILE 3.4 7.2 - - - -
157X ARG* 3.3 71.1 - - + +
158X LYS* 3.9 3.6 - - - -
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Residues in contact with GLU 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X TRP* 1.3 72.7 - - - +
134X VAL* 1.3 72.2 + - - +
135X ALA* 3.2 7.2 + - - +
155X LEU* 3.3 5.2 - - - -
156X ILE* 2.8 46.9 + - + +
158X LYS* 3.8 20.6 - - + +
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Residues in contact with VAL 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129X PHE* 3.8 31.9 - - + -
132X TRP 4.7 0.7 - - - +
133X GLU* 1.3 78.2 - - - +
135X ALA* 1.3 60.1 + - - +
136X SER* 3.7 26.4 - - - +
137X SER* 4.1 13.2 - - - +
153X LEU* 4.4 8.3 - - + -
154X HIS 3.8 2.9 - - - -
155X LEU* 3.8 7.2 - - + -
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Residues in contact with ALA 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X GLU* 3.2 8.4 + - + -
134X VAL* 1.3 71.8 - - - +
136X SER* 1.3 61.8 + - - +
154X HIS* 2.7 32.7 + - - +
156X ILE* 3.7 31.4 - - + -
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Residues in contact with SER 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X VAL* 3.3 10.4 - - - +
135X ALA* 1.3 80.9 - - - +
137X SER* 1.3 62.7 + - - +
138X VAL* 4.8 11.9 - - - +
152X PHE 4.2 1.9 + - - -
153X LEU* 3.5 3.6 - - - -
154X HIS* 3.0 44.5 + - - +
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Residues in contact with SER 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X VAL* 4.1 10.1 - - - +
136X SER* 1.3 75.7 - - - +
138X VAL* 1.3 63.8 + - - +
139X GLU 4.3 0.4 + - - -
151X THR* 3.4 13.2 - - - +
152X PHE 3.4 4.5 - - - -
153X LEU* 3.3 21.7 - - - +
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Residues in contact with VAL 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X SER* 4.8 10.3 - - - +
137X SER* 1.3 82.1 + - - +
139X GLU* 1.3 74.3 + - - +
140X GLY* 3.4 0.7 + - - -
151X THR* 3.4 3.7 - - - +
152X PHE* 2.7 57.2 + - + +
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Residues in contact with GLU 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X SER 4.3 0.4 - - - -
138X VAL* 1.3 81.2 - - - +
140X GLY* 1.3 74.3 + - - +
141X LYS* 3.7 11.3 + - + +
142X LEU* 6.0 1.0 - - - +
150X HIS 3.8 8.1 - - - +
151X THR* 4.4 10.0 - - + +
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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