Contacts of the helix formed by residues 282 - 296 (chain B) in PDB entry 3HTM
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 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ARG* 3.3 27.1 - - + +
222B SER* 4.0 9.9 - - - -
254B MSE 3.3 39.0 - - + -
257B PHE* 4.2 16.2 - - + -
258B ILE* 3.8 27.4 - - + -
277B ALA* 2.9 18.0 + - - +
280B TYR* 3.9 11.0 - - + +
281B ALA* 1.3 69.3 - - - +
283B GLU* 1.3 65.1 + - - +
284B ARG 3.4 2.0 - - - -
285B LEU* 3.2 25.3 + - + -
286B LYS* 3.0 21.5 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 5.8 3.6 - - + -
185A ARG* 5.7 9.6 - - - +
281B ALA* 3.1 9.9 + - - +
282B LEU* 1.3 72.5 - - - +
284B ARG* 1.3 63.3 + - - +
286B LYS* 3.1 27.4 + - - +
287B VAL* 3.1 33.0 + - + +
290B GLU* 5.1 0.7 - - - +
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 4.6 3.8 - - + +
182A PRO* 3.0 44.8 + - + +
183A GLU 3.4 13.9 - - - -
184A CYS* 3.4 30.6 - - - +
185A ARG* 4.6 15.2 - - + +
221B ARG* 5.0 0.8 - - - +
257B PHE* 3.2 29.0 - - + -
261B GLY* 2.9 32.1 + - - -
282B LEU 3.3 0.6 + - - -
283B GLU* 1.3 78.4 - - - +
285B LEU* 1.3 58.0 + - - +
287B VAL* 3.3 3.9 + - - +
288B MSE 2.9 46.2 + - + +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B MSE 4.3 7.2 - - + -
257B PHE* 3.6 51.5 - - + -
263B ALA* 4.0 15.0 - - + -
266B LEU* 4.6 2.2 - - + -
273B LEU* 3.9 41.1 - - + -
277B ALA* 3.8 19.7 - - + -
282B LEU* 3.2 21.1 + - + +
284B ARG* 1.3 77.8 - - - +
286B LYS* 1.3 61.9 + - - +
288B MSE 3.2 9.4 + - - +
289B CYS* 3.0 30.1 + - - -
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Residues in contact with LYS 286 (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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274B LEU* 3.3 25.7 - - + +
277B ALA* 3.7 12.7 - - + +
278B ASP* 2.9 34.6 + - - -
281B ALA* 6.6 0.4 - - - -
282B LEU 3.0 12.2 + - - +
283B GLU* 3.1 29.9 + - - +
285B LEU* 1.3 77.1 - - - +
287B VAL* 1.3 60.9 + - - +
289B CYS* 3.3 1.4 + - - -
290B GLU* 3.1 31.4 + - - +
312B HIS 2.9 20.8 + - - -
313B SER* 2.9 32.3 + - - -
314B ALA* 4.0 4.3 - - - +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.8 12.8 - - + -
180A LYS 3.4 24.7 - - - +
181A VAL* 3.6 16.8 - - + -
182A PRO* 3.6 13.0 - - + -
283B GLU* 3.1 24.9 + - + +
284B ARG 3.3 6.9 + - - +
286B LYS* 1.3 75.3 - - - +
288B MSE 1.3 60.4 + - - +
290B GLU* 3.0 19.1 + - - +
291B ASP* 2.9 26.2 + - - +
316B GLN* 4.1 11.2 - - + +
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Residues in contact with MSE 288 (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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181A VAL* 3.7 22.0 - - + -
257B PHE* 3.9 13.0 - - - -
261B GLY 4.4 8.3 - - - +
262B LYS* 4.7 1.3 - - - -
263B ALA* 4.3 29.6 - - + +
266B LEU* 3.7 25.9 - - + +
284B ARG* 2.9 47.7 + - - +
285B LEU* 3.2 11.6 + - - +
287B VAL* 1.3 76.7 - - - +
289B CYS* 1.3 60.5 + - - +
291B ASP* 3.4 9.6 + - - +
292B ALA* 3.3 17.2 + - - +
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Residues in contact with CYS 289 (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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266B LEU* 3.7 21.5 - - - -
270B ALA 3.6 15.0 - - - +
273B LEU* 3.6 40.6 - - - -
274B LEU* 3.6 18.8 - - + -
285B LEU 3.0 19.5 + - - -
286B LYS 3.6 7.4 - - - +
288B MSE 1.3 74.5 - - - +
290B GLU* 1.3 60.8 + - - +
292B ALA* 3.2 2.3 + - - +
293B LEU* 2.9 35.5 + - - +
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.8 9.7 - - + +
274B LEU* 4.0 3.6 - - + -
283B GLU* 5.1 1.0 - - - +
286B LYS* 3.1 26.2 + - - +
287B VAL* 3.0 33.1 + - - +
289B CYS* 1.3 77.8 - - - +
291B ASP* 1.3 55.6 + - - +
293B LEU* 4.6 1.3 - - - -
294B CYS* 2.9 32.1 + - - +
313B SER 5.2 0.2 - - - +
314B ALA* 3.4 30.2 - - + -
315B ASP 4.6 0.5 + - - -
316B GLN* 3.1 18.9 + - - +
317B LEU* 2.9 44.2 + - + +
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Residues in contact with ASP 291 (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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177A ASN* 4.8 10.0 + - - -
178A MSE 4.9 0.3 + - - -
179A VAL* 3.7 28.9 + - + +
181A VAL* 3.9 23.2 - - + +
287B VAL 2.9 12.1 + - - +
288B MSE 3.5 9.9 - - - +
289B CYS 3.2 0.2 - - - -
290B GLU* 1.3 77.8 - - - +
292B ALA* 1.3 60.1 + - - +
294B CYS* 3.5 1.9 + - - +
295B SER* 2.9 34.7 + - - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 4.1 17.7 - - + -
267B ASP* 4.1 21.3 - - - +
270B ALA* 4.1 7.6 - - + -
288B MSE 3.3 10.0 + - - +
289B CYS 3.2 7.3 + - - +
291B ASP* 1.3 77.3 - - - +
293B LEU* 1.3 65.9 + - - +
295B SER* 3.2 15.6 + - - -
296B ASN* 3.3 22.8 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 3.5 31.9 - - + +
271B ASP* 3.9 13.0 - - + +
274B LEU* 3.8 19.1 - - + -
289B CYS 2.9 20.3 + - - +
292B ALA* 1.3 76.4 - - - +
294B CYS* 1.3 64.7 + - - +
296B ASN* 3.0 18.8 + - + +
297B LEU 3.3 8.0 + - - -
305B ILE* 3.7 26.0 - - + +
308B LEU* 3.9 14.1 - - + -
317B LEU* 3.7 34.8 - - + -
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Residues in contact with CYS 294 (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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178A MSE 4.1 15.9 - - - -
179A VAL* 3.6 16.6 - - + -
290B GLU 2.9 19.3 + - - +
291B ASP* 3.7 3.6 - - - +
292B ALA 3.3 0.2 - - - -
293B LEU* 1.3 76.1 - - - +
295B SER* 1.3 62.6 + - - +
297B LEU* 3.2 27.8 + - - +
317B LEU* 3.8 11.6 - - + +
320B GLN* 3.6 36.6 - - + -
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASN 4.9 8.8 + - - -
291B ASP* 2.9 20.6 + - - -
292B ALA* 3.5 10.9 - - - -
293B LEU 3.1 0.4 - - - -
294B CYS* 1.3 79.1 - - - +
296B ASN* 1.3 62.5 + - - +
297B LEU 3.4 1.8 - - - +
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Residues in contact with ASN 296 (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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267B ASP* 5.2 8.1 + - - +
270B ALA* 5.7 2.0 - - - +
292B ALA* 3.3 21.2 + - - +
293B LEU* 3.0 15.7 + - + +
295B SER* 1.3 83.0 - - - +
297B LEU* 1.3 59.4 + - - +
298B SER* 3.1 3.3 + - - -
301B ASN* 2.6 34.3 + - - +
305B ILE* 4.7 2.5 - - + -
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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