Contacts of the helix formed by residues 140 - 145 (chain A) in PDB entry 1CS8
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASP* 3.1 37.4 + - - -
138A ALA 3.4 1.0 - - - -
139A GLY* 1.3 80.1 - - - +
141A GLU* 1.3 62.3 + - + +
142A SER* 3.7 17.9 - - - +
143A PHE* 2.9 20.0 + - - +
144A LEU* 3.2 15.3 + - - +
151A TYR* 4.0 5.4 - - - +
153A GLU* 4.1 11.4 - - + +
155A ASP* 3.3 40.2 + - + +
156A CYS* 3.8 14.6 - - - -
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Residues in contact with GLU 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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37A LYS* 4.9 9.8 + - - -
38A ASN* 4.7 4.6 - - - +
41A MET* 3.4 45.2 - - + +
58A MET* 3.6 4.6 - - - +
68A SER* 5.0 14.4 - - - -
139A GLY 4.0 1.2 + - - -
140A HIS* 1.3 72.5 - - + +
142A SER* 1.3 64.6 + - - +
144A LEU* 4.3 12.3 - - + +
145A PHE* 3.2 31.2 + - + -
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Residues in contact with SER 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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45A HIS* 5.4 2.0 - - - -
56A PHE* 3.8 26.3 - - - -
58A MET* 3.9 17.2 - - - +
140A HIS* 3.7 2.8 - - - +
141A GLU* 1.3 82.5 - - - +
143A PHE* 1.3 55.6 + - - +
145A PHE 4.0 1.0 - - - -
146A TYR* 3.3 25.5 + - - +
151A TYR* 2.9 25.2 + - - -
153A GLU* 2.7 28.0 + - - -
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Residues in contact with PHE 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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136A ILE* 3.8 18.8 - - + -
137A ASP 5.4 0.9 - - - -
138A ALA* 3.6 33.4 - - + +
140A HIS 2.9 9.8 + - - +
142A SER* 1.3 78.6 + - - +
144A LEU* 1.3 66.3 + - - +
145A PHE 3.1 2.4 + - - -
146A TYR* 3.2 7.5 + - + +
151A TYR* 3.4 36.1 - + - +
163A HIS* 4.4 3.6 - + - -
165A VAL* 5.6 0.7 - - + -
187A ASN* 3.9 7.9 - - - -
189A TRP* 3.6 30.1 - + - -
193A TRP* 3.2 48.0 + + - -
199A VAL* 4.2 10.3 - - + -
201A MET* 3.7 24.7 - - + -
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Residues in contact with LEU 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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61A ASN* 3.0 18.4 + - - -
63A PHE* 3.8 9.3 - - + -
66A MET 5.9 1.6 - - - +
67A THR 5.1 0.7 - - - +
68A SER* 4.1 22.4 - - - +
71A PHE* 3.7 54.3 - - + -
72A ARG* 5.9 0.7 - - + -
138A ALA 3.5 21.3 - - - +
139A GLY* 4.4 3.8 - - - +
140A HIS 3.2 20.4 + - - +
141A GLU* 3.8 12.8 - - + +
143A PHE* 1.3 75.9 - - - +
145A PHE* 1.3 76.8 + - + +
189A TRP* 4.3 6.5 - - + -
193A TRP* 3.2 12.6 + - - +
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Residues in contact with PHE 145 (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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38A ASN* 3.8 33.2 - - + -
41A MET* 3.9 15.3 - - + -
42A ILE* 4.0 14.4 - - + -
58A MET* 3.2 19.6 - - + -
59A ALA 2.9 41.7 + - - +
60A MET* 4.5 3.4 - - - -
61A ASN* 3.4 33.2 - - - +
63A PHE* 3.7 23.6 - - + -
64A GLY* 3.9 14.8 - - - -
66A MET 5.0 1.6 - - - -
141A GLU* 3.2 18.7 + - + -
142A SER 4.0 2.7 - - - -
143A PHE 3.1 0.4 - - - -
144A LEU* 1.3 91.6 - - + +
146A TYR* 1.3 60.3 + - - +
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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