Contacts of the strand formed by residues 239 - 243 (chain A) in PDB entry 3ROT
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 GLN 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU 5.6 0.3 - - - +
146A THR* 3.4 34.1 - - + +
148A SER* 5.8 0.4 - - - +
209A ASN* 2.8 19.3 + - + +
210A ILE* 3.2 4.4 - - + +
211A ILE 2.7 30.8 + - - +
237A GLN 3.6 10.9 + - - -
238A PRO* 1.3 79.3 + - + +
240A VAL* 1.3 55.2 + - - +
241A TYR* 4.0 7.6 - - + -
259A ASN* 3.1 28.0 + - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 3.3 13.0 - - + +
213A CYS* 4.3 2.7 - - - -
219A LEU* 3.8 29.2 - - + -
222A LEU* 4.2 11.7 - - + -
226A LEU* 4.1 14.4 - - + -
238A PRO* 3.6 23.5 + - + +
239A GLN* 1.3 76.6 - - - +
241A TYR* 1.3 78.2 + - - +
257A LEU 3.7 22.2 + - - +
258A VAL* 3.5 9.5 - - + +
259A ASN* 2.8 32.9 + - - +
260A TYR 3.9 0.2 + - - -
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Residues in contact with TYR 241 (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* 4.1 12.1 - - + -
142A ALA* 3.3 40.8 + - + -
145A LEU* 3.4 14.4 - - + +
146A THR* 2.6 29.1 + - - -
210A ILE* 3.9 12.6 - - + -
211A ILE 2.7 15.0 + - - +
212A PHE* 3.4 21.0 - + + -
213A CYS* 2.7 27.1 + - - +
239A GLN* 4.0 15.5 - - + -
240A VAL* 1.3 79.9 - - - +
242A SER* 1.3 64.8 + - - +
258A VAL* 4.8 0.4 - - - -
259A ASN* 3.1 29.4 + - + -
260A TYR* 3.5 27.6 - - + +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.6 10.3 - - - +
213A CYS* 3.3 25.8 + - - +
215A THR 3.9 5.9 + - - -
216A SER* 4.5 0.3 + - - -
219A LEU* 3.8 28.8 - - - +
241A TYR* 1.3 77.6 - - - +
243A PHE* 1.3 80.2 + - - +
249A THR* 5.0 0.2 - - - -
258A VAL* 5.0 1.1 - - - -
260A TYR 3.2 8.3 + - - -
261A VAL* 3.3 15.2 - - - +
262A MSE 2.9 21.7 + - - -
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Residues in contact with PHE 243 (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 ALA* 3.9 16.4 - - + -
135A GLY* 4.2 15.0 - - - -
138A LEU* 3.3 25.6 - - + -
167A ARG* 3.6 51.4 - - + +
171A ILE* 4.2 10.8 - - + -
213A CYS 3.4 15.4 + - - -
214A LEU* 3.5 22.4 - - + +
216A SER* 3.8 10.6 + - - -
242A SER* 1.3 89.3 + - - +
244A ASP* 1.3 81.1 + - - +
261A VAL* 3.7 1.8 - - - -
262A MSE 3.6 25.6 - - + -
264A GLN* 5.0 6.7 - - + -
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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