Contacts of the helix formed by residues 124 - 131 (chain b) in PDB entry 4RO0
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 SER 124 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B PHE* 5.2 8.3 - - - -
123b TRP* 1.3 84.8 - - - +
125b GLU* 1.3 64.0 + - - +
126b SER* 3.1 17.2 + - - -
127b THR* 3.1 17.1 + - - +
128b LEU* 3.2 10.0 + - - +
184b ASP* 2.7 29.5 + - - -
210b GLU* 4.9 0.4 + - - -
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Residues in contact with GLU 125 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLU* 3.4 51.7 + - + +
213B ARG* 3.9 14.7 + - - +
214B TYR 4.6 0.5 + - - -
232B PHE* 4.1 11.4 - - + -
166a ARG* 2.7 36.5 + - - -
124b SER* 1.3 75.2 - - - +
126b SER* 1.3 57.4 + - - +
128b LEU* 3.1 24.0 + - - +
129b GLU* 2.9 40.5 + - + +
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Residues in contact with SER 126 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B PHE* 3.2 34.1 - - - -
235B SER* 3.7 12.8 + - - -
236B GLY* 3.2 13.0 - - - -
239B MET* 4.1 6.7 - - - -
124b SER* 3.1 10.5 + - - -
125b GLU* 1.3 78.2 - - - +
127b THR* 1.3 58.3 + - - +
129b GLU 3.3 1.7 + - - -
130b CYS* 2.9 23.4 + - - +
184b ASP* 3.6 4.5 - - - -
210b GLU* 3.0 27.4 + - - -
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Residues in contact with THR 127 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B MET* 4.6 9.2 - - - -
120b ILE* 3.6 34.5 - - + +
122b GLY 4.0 4.9 - - - +
123b TRP* 3.1 19.3 - - - -
124b SER 3.1 22.6 + - - +
126b SER* 1.3 74.1 - - - +
128b LEU* 1.3 62.6 + - - +
130b CYS* 3.3 10.7 - - - +
131b LEU* 3.3 26.7 + - - +
182b ILE* 5.0 0.7 - - + -
184b ASP* 3.8 30.3 - - + +
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Residues in contact with LEU 128 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166a ARG* 3.8 17.5 - - - +
123b TRP* 3.6 21.0 - - + +
124b SER 3.2 13.4 + - - +
125b GLU* 3.1 38.1 + - - +
127b THR* 1.3 75.2 + - - +
129b GLU* 1.3 63.9 - - - +
131b LEU* 3.0 23.6 + - - +
132b ARG* 3.7 5.9 + - - +
151b LYS 5.2 0.4 - - - +
155b SER* 3.3 28.3 - - - +
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Residues in contact with GLU 129 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B TYR* 3.7 28.1 + - - +
232B PHE 3.9 18.4 - - - +
233B VAL* 4.0 19.0 - - + +
236B GLY* 4.1 11.9 - - - +
237B ARG* 4.7 3.1 + - + +
240B SER* 5.0 1.7 + - - -
125b GLU* 2.9 30.9 + - + +
126b SER 3.6 8.1 - - - +
128b LEU* 1.3 79.3 - - - +
130b CYS* 1.3 62.5 + - - +
132b ARG* 3.3 53.9 + - - +
133b GLU* 4.6 1.4 + - - +
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Residues in contact with CYS 130 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B GLY* 3.5 15.2 + - - +
239B MET* 3.9 17.0 - - + -
240B SER* 3.5 17.1 - - - -
120b ILE* 4.6 7.0 - - - -
126b SER 2.9 13.3 + - - +
127b THR* 3.3 17.0 - - - +
129b GLU* 1.3 77.9 - - - +
131b LEU* 1.3 56.5 + - - +
132b ARG 3.2 4.1 + - - -
133b GLU 3.4 9.9 + - - -
134b LEU* 3.7 19.8 - - - +
182b ILE* 3.7 30.1 - - - -
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Residues in contact with LEU 131 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120b ILE* 4.5 10.3 - - + -
123b TRP* 3.6 38.6 - - + -
127b THR 3.3 4.9 + - - +
128b LEU 3.0 11.7 + - - +
130b CYS* 1.3 74.7 - - - +
132b ARG* 1.3 59.8 + - - +
133b GLU 3.2 1.8 - - - -
134b LEU* 3.9 12.3 - - + +
135b ARG* 3.1 34.4 + - - +
139b VAL* 3.8 38.1 - - + -
141b VAL* 4.9 0.7 - - + -
155b SER* 3.8 25.6 - - - +
156b GLY 5.7 0.9 - - - +
157b ALA* 4.0 17.5 - - + -
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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