Contacts of the helix formed by residues 264 - 271 (chain B) in PDB entry 3L2W
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 THR 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ASN 3.6 13.2 - - - -
255B ASN* 3.4 31.9 + - + +
256B THR 3.7 2.7 - - - +
257B TYR* 3.6 29.4 - - + -
263B TYR* 1.3 74.1 - - - +
265B PRO* 1.3 72.3 - - - +
266B HIS* 3.8 5.0 + - - +
267B GLN* 2.8 46.1 + - - +
268B LEU* 3.1 13.5 + - - +
274B SER* 4.7 1.6 + - - -
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Residues in contact with PRO 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B THR* 3.6 23.7 - - - +
151B GLY* 3.6 26.0 - - - +
152B PHE* 3.7 16.1 - - + +
219B LYS* 6.0 1.1 - - - -
223B LYS* 4.2 7.9 - - - +
253B LEU 4.0 5.2 - - - +
254B ASN* 3.4 22.0 - - - +
256B THR 3.3 16.8 - - - +
258B SER* 5.1 5.2 - - - +
263B TYR 4.0 3.6 - - - +
264B THR* 1.3 81.9 - - - +
266B HIS* 1.3 64.2 + - - +
267B GLN 3.2 0.2 + - - -
268B LEU* 3.2 4.4 + - + +
269B LEU* 3.0 25.5 + - - +
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Residues in contact with HIS 266 (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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122A PHE* 4.8 6.5 - + + +
176A ILE 4.4 5.8 - - - -
177A ALA* 3.7 26.2 - - + +
152B PHE* 3.9 12.5 - + + -
254B ASN* 2.8 19.6 + - + +
255B ASN* 3.6 17.0 - - - +
264B THR* 3.0 3.3 + - - +
265B PRO* 1.3 74.9 - - - +
267B GLN* 1.3 57.6 + - - +
270B PHE* 3.0 62.5 + + - +
272B ILE* 3.4 16.5 + - + -
273B ASP 3.0 25.3 - - - -
274B SER* 3.0 25.9 + - - -
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Residues in contact with GLN 267 (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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292A LEU* 3.6 4.7 - - - +
257B TYR* 3.9 18.9 + - - -
263B TYR* 3.3 29.0 - - + -
264B THR* 2.8 43.3 + - - +
266B HIS* 1.3 75.1 - - - +
268B LEU* 1.3 61.4 + - - +
271B GLY* 2.8 30.7 + - - -
272B ILE 3.4 25.6 - - - +
273B ASP* 3.3 27.2 + - - +
274B SER* 5.5 0.6 - - - +
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Residues in contact with LEU 268 (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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288A ARG* 2.9 34.8 + - + -
289A GLU* 5.8 5.6 - - + +
292A LEU* 3.5 15.4 - - + +
149B MET* 4.5 17.9 - - + +
150B THR* 3.7 41.6 - - + +
219B LYS* 4.4 14.6 - - - +
261B LEU* 4.7 15.3 - - + +
263B TYR* 3.8 37.0 - - + +
264B THR 3.1 14.4 + - - +
265B PRO* 3.8 5.2 - - + +
267B GLN* 1.3 77.3 - - - +
269B LEU* 1.3 58.9 + - - +
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Residues in contact with LEU 269 (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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176A ILE* 5.7 0.2 - - + -
270A PHE* 3.5 46.3 - - + +
288A ARG* 2.9 19.0 + - - +
121B PRO* 4.4 14.8 - - + -
122B PHE* 4.0 17.7 - - + -
147B ASP* 5.9 1.3 - - - +
150B THR* 4.3 9.6 - - + +
152B PHE* 3.6 33.9 - - + -
154B TRP* 4.6 9.6 - - + -
265B PRO 3.0 15.9 + - - +
266B HIS 3.9 2.5 - - - +
268B LEU* 1.3 77.9 - - - +
270B PHE* 1.3 82.6 + - + +
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Residues in contact with PHE 270 (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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121A PRO* 5.4 0.4 - - + -
122A PHE* 4.0 15.0 - + + -
176A ILE* 3.8 24.5 - - + -
269A LEU* 3.5 37.5 - - + +
270A PHE* 3.6 23.3 - + - -
292A LEU* 4.3 2.7 - - - -
295A LEU* 4.0 2.7 - - - +
299A ARG* 3.0 33.4 + - - +
152B PHE* 3.9 11.0 - + - -
266B HIS* 3.0 53.2 + + + +
269B LEU* 1.3 100.2 - - + +
271B GLY* 1.3 59.7 + - - +
272B ILE* 4.1 17.6 - - + +
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Residues in contact with GLY 271 (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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292A LEU* 3.4 28.3 - - - +
295A LEU* 5.0 0.2 - - - -
296A GLN* 2.9 27.5 + - - +
299A ARG* 3.5 10.9 + - - -
267B GLN 2.8 18.6 + - - -
269B LEU 3.6 1.0 - - - -
270B PHE* 1.3 74.2 - - - +
272B ILE* 1.3 61.6 - - - +
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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