Contacts of the helix formed by residues 138 - 144 (chain A) in PDB entry 5C58
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 HIS 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 3.2 21.7 - - - +
137A ARG* 1.3 84.3 - - - +
139A ALA* 1.3 76.6 + - + +
140A ALA* 3.0 19.9 + - + +
141A ASP* 3.2 22.3 + - - +
153A VAL* 3.5 24.3 - - + +
155A GLN* 3.2 35.0 - - - +
157A ASP 2.7 28.2 + - - -
158A PRO* 3.3 19.6 - - + +
159A ALA 3.0 24.9 + - - -
280A ARG* 5.7 1.8 - - - -
322A TYR* 4.2 3.8 - + - -
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 5.3 0.4 - - - -
138A HIS* 1.3 79.1 + - - +
140A ALA* 1.3 55.9 + - - +
141A ASP 3.3 1.8 - - - -
142A ILE* 3.2 34.0 - - + +
158A PRO* 4.6 9.5 + - - +
160A LEU* 3.8 28.9 - - + +
198A ILE* 4.0 22.9 - - + +
199A ASP 5.8 0.4 - - - -
200A SER* 5.2 9.4 - - - -
280A ARG* 6.2 1.3 - - - -
322A TYR* 4.8 3.0 + - - -
324A MET* 6.3 1.3 - - - -
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A HIS* 3.0 19.3 + - + +
139A ALA* 1.3 76.3 - - - +
141A ASP* 1.3 60.7 + - - +
142A ILE 3.2 5.3 + - - -
143A LEU* 3.9 17.5 + - - +
144A GLU* 4.3 7.6 - - - +
151A SER* 3.6 30.1 - - - +
153A VAL* 3.6 21.1 - - + +
159A ALA 5.2 0.4 - - - +
160A LEU* 3.9 11.2 - - + -
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.0 33.4 + - - +
136A ALA* 3.6 13.2 - - + +
137A ARG* 3.9 6.6 + - - +
138A HIS* 3.2 43.2 + - - +
140A ALA* 1.3 79.5 - - - +
142A ILE* 1.3 57.2 + - - +
143A LEU 3.2 7.5 + - - -
144A GLU* 3.8 23.3 + - - +
153A VAL* 4.9 1.4 - - - +
155A GLN* 3.5 16.2 + - - -
832A GLU* 3.7 18.7 - - - +
853A ARG* 4.9 2.4 - - - -
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.1 36.4 - - + +
130A GLN* 4.4 2.2 - - - +
131A MET* 3.7 36.3 - - + -
134A ARG* 4.5 6.7 - - - +
136A ALA* 4.0 20.2 - - + -
139A ALA* 3.2 24.7 - - + +
141A ASP* 1.3 80.3 - - - +
143A LEU* 1.3 71.1 + - + +
144A GLU 3.6 0.9 - - - -
145A GLN 5.1 0.2 - - - -
146A THR* 5.0 2.1 - - - +
160A LEU* 5.8 0.2 - - + -
198A ILE* 6.3 0.7 - - + -
200A SER* 4.6 8.1 - - - +
203A LEU* 5.0 2.2 - - + -
206A VAL* 4.7 7.2 - - + -
228A PHE* 4.2 25.4 - - + -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 5.5 2.9 - - + -
139A ALA 5.2 0.4 - - - +
140A ALA* 4.2 11.4 - - - +
141A ASP 3.2 1.2 - - - -
142A ILE* 1.3 99.4 - - + +
144A GLU* 1.3 53.6 - - - +
145A GLN 2.9 11.9 + - - -
146A THR* 3.2 20.1 + - - +
149A ALA* 3.9 12.1 - - + +
150A TYR* 3.6 27.1 - - - +
151A SER* 4.4 9.6 - - - -
160A LEU* 4.9 7.4 - - + -
162A VAL* 4.2 22.4 - - + -
206A VAL* 5.7 0.9 - - + -
208A ILE* 3.7 28.5 - - + -
228A PHE* 5.4 4.3 - - + -
766A ARG* 2.6 28.2 + - - +
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 4.1 8.2 + - - +
140A ALA 4.3 8.2 - - - +
141A ASP* 3.8 35.4 + - - +
142A ILE 3.6 1.0 - - - -
143A LEU* 1.3 76.0 - - - +
145A GLN* 1.3 58.5 + - - +
146A THR 5.0 0.4 - - - -
704A THR* 5.3 0.2 + - - -
766A ARG* 3.4 33.2 + - - +
767A GLY 4.9 3.1 - - - +
768A SER* 4.2 13.2 - - - -
787A ARG* 3.0 49.4 + - + +
810A TYR* 4.6 9.7 + - - +
839A TYR* 5.5 2.1 + - - -
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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