Contacts of the helix formed by residues 250 - 255 (chain B) in PDB entry 3R2W
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 LEU 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 4.7 20.9 - - + -
87B PRO* 3.8 24.1 - - + +
91B SER* 5.3 6.1 - - - +
93B VAL* 6.4 0.2 - - + -
94B LEU* 3.9 31.6 - - + -
138B LEU* 5.9 2.7 - - + -
142B TYR* 3.8 31.9 - - + +
248B VAL* 4.1 6.9 + - + +
249B ASP* 1.3 76.2 + - - +
251B TYR* 1.3 62.1 + - + +
253B LEU* 3.0 15.1 + - + +
254B ASN* 2.9 27.7 + - - +
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Residues in contact with TYR 251 (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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78B TYR* 4.1 10.3 - - + +
81B ILE* 3.5 15.0 - - + +
82B LYS* 2.9 45.3 - - + +
85B GLY* 3.4 17.4 - - - +
86B LEU* 3.4 48.2 - - + +
249B ASP* 3.3 19.2 - - - +
250B LEU* 1.3 78.2 - - + +
252B ILE* 1.3 59.0 + - - +
253B LEU 3.0 4.2 + - - -
254B ASN* 3.2 20.6 + - - +
255B HIS 3.4 4.5 + - - -
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 4.8 4.9 - - + -
81B ILE* 4.3 10.5 - - + -
249B ASP* 3.2 33.7 + - + +
251B TYR* 1.3 77.2 - - - +
253B LEU* 1.3 57.1 + - - +
254B ASN 3.5 0.2 - - - -
255B HIS* 4.0 6.8 + - + +
256B LEU* 3.2 23.3 - - + +
268B VAL* 4.1 14.8 - - + -
270B GLU* 4.1 13.2 - - + +
322B TRP* 3.5 37.5 - - + +
374B ILE* 3.2 41.7 - - + -
380B ARG* 4.5 5.2 - - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO* 5.9 0.7 - - + -
93B VAL* 3.9 19.7 - - + +
94B LEU* 3.8 28.5 - - + -
97B LEU* 4.0 18.8 - - + -
235B TYR* 5.4 1.3 - - + -
248B VAL* 5.0 2.7 - - + -
249B ASP 3.4 9.1 + - - +
250B LEU* 3.0 19.9 + - + +
252B ILE* 1.3 76.8 - - - +
254B ASN* 1.3 60.8 + - - +
255B HIS 3.1 2.0 - - - -
256B LEU* 3.6 7.5 - - + +
257B MET* 3.0 56.0 + - + +
322B TRP* 3.4 31.4 - - + -
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Residues in contact with ASN 254 (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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84B ARG* 4.9 7.3 + - - +
85B GLY 2.5 30.5 + - - +
86B LEU 4.0 1.0 + - - -
87B PRO* 3.2 36.2 - - + +
93B VAL* 5.3 0.7 - - - -
250B LEU 2.9 11.5 + - - +
251B TYR 3.2 15.2 + - - +
253B LEU* 1.3 78.0 - - - +
255B HIS* 1.3 53.5 - - - +
256B LEU 3.2 0.9 - - - -
257B MET* 2.8 16.7 - - - +
258B ASN* 3.0 34.5 - - - +
260B PRO* 4.9 0.5 - - - +
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Residues in contact with HIS 255 (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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76B GLN* 3.6 28.5 + - - -
81B ILE* 4.1 26.8 - - + +
84B ARG* 3.3 29.5 + - - -
251B TYR 3.4 9.9 + - - +
252B ILE* 4.4 8.1 - - + +
253B LEU 3.1 1.2 - - - +
254B ASN* 1.3 78.3 - - - +
256B LEU* 1.3 62.0 + - + +
257B MET 3.7 2.5 - - - -
259B PRO* 3.6 14.7 - - + +
260B PRO* 3.8 22.0 - - + +
263B LYS 5.9 0.8 + - - -
265B CYS 5.1 1.6 - - - +
268B VAL* 5.4 7.6 - - + -
372B LEU* 4.2 17.8 - - + +
374B ILE* 5.8 0.7 - - + -
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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