Contacts of the helix formed by residues 254 - 267 (chain B) in PDB entry 3SN5
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 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.7 22.2 - - - -
186B THR 3.5 15.1 + - - -
187B ILE* 2.9 27.9 + - - +
252B SER 3.7 2.0 + - - -
253B ILE* 1.3 77.8 - - - +
255B GLU* 1.3 63.6 + - - +
256B LEU* 3.5 9.4 + - - +
257B ILE* 3.1 17.2 + - - +
258B SER* 3.0 21.9 + - - -
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR* 3.6 8.6 - - + +
137B ALA* 4.1 32.1 + - + +
140B SER* 5.2 6.5 - - - +
141B LEU* 5.6 0.6 - - - +
253B ILE 3.8 1.0 + - - -
254B SER* 1.3 71.2 - - - +
256B LEU* 1.3 52.2 + - - +
258B SER* 3.4 10.2 + - - +
259B LEU* 2.9 36.7 + - - +
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Residues in contact with LEU 256 (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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128B THR* 4.5 3.5 - - + +
129B PHE* 3.7 27.4 - - + -
132B THR* 3.3 35.1 + - - +
133B LEU* 4.3 13.7 - - + -
141B LEU* 5.9 1.3 - - + -
187B ILE* 4.7 10.8 - - + -
254B SER* 3.1 9.1 + - - +
255B GLU* 1.3 77.8 - - - +
257B ILE* 1.3 64.7 + - + +
259B LEU* 3.3 3.3 + - - +
260B ARG* 2.8 45.9 + - + +
282B VAL* 3.8 23.6 - - + -
601B HEM 4.1 20.0 - - + -
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Residues in contact with ILE 257 (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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187B ILE* 3.4 35.9 - - + +
188B PHE* 3.7 28.5 - - + -
247B LEU* 4.1 12.3 - - + -
253B ILE* 3.8 13.5 - - + -
254B SER* 3.1 3.5 + - - +
256B LEU* 1.3 76.2 - - + +
258B SER* 1.3 61.0 + - - +
260B ARG* 3.2 6.2 + - + +
261B MET* 2.8 44.3 + - + +
279B HIS* 3.9 17.0 - - - +
282B VAL* 3.7 31.6 - - + -
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Residues in contact with SER 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ILE* 3.8 16.1 + - - +
254B SER 3.0 15.5 + - - -
255B GLU* 3.4 15.6 + - - +
257B ILE* 1.3 74.4 - - - +
259B LEU* 1.4 63.8 + - - +
261B MET* 3.4 10.6 + - - +
262B PHE* 3.1 23.3 + - - +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B THR* 4.2 16.2 - - + +
131B LYS* 4.3 23.8 - - + +
132B THR* 3.8 21.1 - - + -
255B GLU 2.9 19.7 + - - +
256B LEU 3.7 3.1 - - - +
258B SER* 1.4 76.2 + - - +
260B ARG* 1.3 52.3 + - - +
262B PHE* 3.2 12.9 + - + +
263B LEU* 2.9 67.2 + - + +
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Residues in contact with ARG 260 (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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123B GLU* 2.7 41.2 + - - -
125B ILE* 5.0 0.4 - - - +
128B THR* 3.7 20.4 - - + -
129B PHE* 4.6 4.0 - - - -
256B LEU* 2.8 35.9 + - + +
257B ILE* 3.6 10.3 - - + +
259B LEU* 1.3 70.3 - - - +
261B MET* 1.3 57.2 + - - +
263B LEU* 4.6 1.8 - - - +
264B ASN* 2.8 58.5 + - - +
270B PHE* 5.9 1.2 - - - -
278B THR* 3.1 33.5 + - - +
279B HIS* 4.0 16.6 + - + +
282B VAL* 4.5 11.9 - - - -
1429B K2B 3.7 24.8 - - - +
2123B UNX 4.5 0.6 - - - -
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Residues in contact with MET 261 (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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244B HIS* 3.3 55.2 - - + +
247B LEU* 3.9 23.8 - - + -
248B GLN* 3.7 33.9 - - + +
253B ILE* 4.8 9.6 - - + -
257B ILE* 2.8 30.4 + - + +
258B SER* 3.7 10.3 - - - +
260B ARG* 1.3 69.6 - - - +
262B PHE* 1.3 65.7 + - - +
264B ASN 3.2 1.7 + - - -
265B ASP* 3.2 22.5 + - - +
279B HIS* 3.6 11.7 - - + +
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Residues in contact with PHE 262 (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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258B SER 3.1 10.9 + - - +
259B LEU* 3.4 16.8 - - + +
261B MET* 1.3 78.4 - - - +
263B LEU* 1.4 69.3 + - + +
265B ASP* 3.2 9.2 + - + +
266B THR* 2.9 54.6 + - + -
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Residues in contact with LEU 263 (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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123B GLU* 3.4 27.6 - - + +
128B THR* 3.4 26.9 - - + +
259B LEU* 2.9 49.2 + - + +
260B ARG 4.3 1.8 - - - +
262B PHE* 1.4 79.4 - - + +
264B ASN* 1.3 59.9 + - - +
266B THR* 4.4 5.6 - - + +
267B LEU* 2.8 48.2 + - + +
2123B UNX 3.1 13.3 - - - -
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Residues in contact with ASN 264 (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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244B HIS* 3.5 24.8 + - + -
260B ARG* 2.8 46.9 + - - +
261B MET 3.2 6.9 + - - +
263B LEU* 1.3 75.0 - - - +
265B ASP* 1.3 59.7 + - - +
268B SER* 2.6 31.2 + - - +
270B PHE* 4.4 12.7 - - - -
275B LYS* 3.4 27.2 + - + +
278B THR* 3.1 23.6 + - - +
279B HIS* 3.5 8.3 + - - -
2123B UNX 4.1 1.1 - - - -
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B HIS* 3.4 21.6 + - - -
248B GLN* 5.2 5.5 + - - -
261B MET* 3.2 13.4 + - - +
262B PHE* 3.2 9.9 + - + +
264B ASN* 1.3 78.5 - - - +
266B THR* 1.3 61.8 + - - +
268B SER 4.2 6.8 - - - +
275B LYS* 2.8 30.6 + - - +
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Residues in contact with THR 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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262B PHE* 2.9 44.8 + - + -
263B LEU* 4.4 3.4 - - + -
265B ASP* 1.3 78.9 - - - +
267B LEU* 1.3 82.2 + - + +
268B SER 3.7 0.7 - - - -
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Residues in contact with LEU 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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120B ASN 4.2 0.2 - - - +
121B THR* 3.2 21.2 - - - +
122B THR* 3.2 28.0 + - - +
123B GLU* 4.2 23.6 - - + +
263B LEU* 2.8 38.3 + - + +
266B THR* 1.3 93.5 - - + +
268B SER* 1.3 59.3 + - - +
2123B UNX 3.6 5.8 - - - -
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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