Contacts of the helix formed by residues 200 - 210 (chain A) in PDB entry 3RBQ
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PRO 4.1 0.8 + - - -
199A LEU* 1.3 76.1 - - - +
201A GLU* 1.3 64.3 + - - +
202A GLU* 3.6 9.4 + - - +
203A LEU* 3.1 28.0 + - - +
204A ILE* 3.0 19.8 + - - +
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Residues in contact with GLU 201 (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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139A ARG* 2.7 46.0 + - - -
199A LEU 4.9 1.9 - - - +
200A SER* 1.3 74.0 - - - +
202A GLU* 1.3 62.4 + - - +
204A ILE* 3.9 7.0 - - - +
205A SER* 3.1 25.7 + - - -
205B SER* 4.1 16.5 + - - +
209B ARG* 4.0 9.6 + - - -
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Residues in contact with GLU 202 (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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200A SER* 3.2 8.1 + - - +
201A GLU* 1.3 78.8 - - - +
203A LEU* 1.3 61.0 + - - +
205A SER* 3.0 20.2 + - - +
206A GLU* 3.1 40.7 + - + +
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Residues in contact with LEU 203 (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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167A PHE* 3.8 27.8 - - + -
170A GLN* 4.1 30.3 - - - +
172A LEU* 3.8 20.2 - - + -
199A LEU* 4.1 16.2 - - + -
200A SER* 3.1 25.0 + - - +
202A GLU* 1.3 75.0 + - - +
204A ILE* 1.3 60.7 + - - +
206A GLU* 3.2 16.8 + - - +
207A MET* 2.8 48.9 + - - +
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Residues in contact with ILE 204 (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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135A PRO 5.2 0.9 - - - +
138A LEU* 4.0 24.5 - - + +
139A ARG* 3.7 53.2 - - + +
199A LEU* 3.6 39.7 - - + +
200A SER 3.0 16.9 + - - +
201A GLU* 3.9 8.7 - - - +
203A LEU* 1.3 77.0 - - - +
205A SER* 1.3 64.7 + - - +
207A MET* 3.9 3.5 - - - +
208A ILE* 3.1 42.4 + - + +
205B SER* 6.4 0.9 - - - -
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Residues in contact with SER 205 (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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201A GLU 3.1 14.7 + - - -
202A GLU* 3.0 19.2 + - - +
204A ILE* 1.3 78.3 - - - +
206A GLU* 1.3 57.4 + - - +
208A ILE* 3.3 9.5 + - - +
209A ARG* 2.9 34.6 + - - +
139B ARG* 4.4 6.4 + - - -
201B GLU* 4.0 25.9 + - - +
204B ILE* 6.4 0.4 - - - -
205B SER* 5.5 11.4 - - - -
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Residues in contact with GLU 206 (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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167A PHE* 3.8 21.3 - - + -
168A ARG* 5.8 3.6 - - - +
170A GLN* 5.6 0.3 - - - +
202A GLU* 3.1 50.1 + - + +
203A LEU* 3.6 23.7 - - - +
205A SER* 1.3 78.8 - - - +
207A MET* 1.3 57.7 + - - +
209A ARG* 3.2 7.1 + - - +
210A HIS* 3.0 46.4 + - + +
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Residues in contact with MET 207 (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 LEU* 3.6 29.6 - - + -
167A PHE* 3.6 31.6 - - + -
172A LEU* 3.5 28.5 - - + -
199A LEU* 4.0 18.4 - - + -
203A LEU* 2.8 42.2 + - + +
204A ILE* 3.9 4.3 - - - +
206A GLU* 1.3 74.9 - - - +
208A ILE* 1.3 61.9 + - - +
210A HIS 3.6 14.0 + - - +
211A PRO* 4.2 2.4 - - - +
214A THR* 3.4 24.2 + - + +
236A TYR* 3.8 19.3 + - + +
500G DAO 5.1 2.2 - - + -
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Residues in contact with ILE 208 (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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135A PRO* 3.6 27.8 - - + +
138A LEU* 3.8 13.7 - - + -
204A ILE* 3.1 38.3 + - + +
205A SER* 3.6 7.9 - - - +
207A MET* 1.3 75.7 - - - +
209A ARG* 1.3 65.4 + - + +
210A HIS 3.5 0.5 + - - -
211A PRO* 3.9 1.6 - - - +
236A TYR* 4.0 11.9 - - + +
237A SER* 3.3 19.8 + - - -
135B PRO* 3.5 36.6 - - + -
208B ILE* 4.4 18.8 - - + -
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Residues in contact with ARG 209 (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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205A SER* 2.9 21.6 + - - +
206A GLU* 3.6 10.1 - - - +
208A ILE* 1.3 79.7 - - + +
210A HIS* 1.3 80.4 + - + +
211A PRO* 3.3 8.8 - - - +
139B ARG* 3.3 51.7 - - - +
201B GLU* 3.5 23.6 + - - -
106F LYS* 5.8 5.7 - - - +
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Residues in contact with HIS 210 (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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167A PHE* 4.0 11.3 - + + -
168A ARG* 3.4 35.9 + - - -
206A GLU* 3.0 34.3 + - + +
207A MET 3.8 8.5 - - - +
208A ILE 3.3 0.6 - - - -
209A ARG* 1.3 104.2 + - + +
211A PRO* 1.4 67.8 - - - +
212A TYR 3.5 0.2 + - - -
213A GLU* 3.2 35.7 + - - +
214A THR* 4.4 1.2 + - - -
234A TYR 5.0 0.2 - - - +
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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