Contacts of the helix formed by residues 291 - 300 (chain B) in PDB entry 6TX0
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 PRO 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B TRP* 3.5 13.0 - - + +
290B ARG* 1.4 96.2 - - + +
292B GLU* 1.3 55.3 + - - +
293B ASN* 3.1 26.0 - - - +
294B LYS* 2.7 37.8 + - + -
295B SER 3.8 0.3 + - - -
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Residues in contact with GLU 292 (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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284B LEU* 5.3 1.0 - - - -
285B TRP* 3.6 53.9 + - + +
291B PRO* 1.3 72.4 - - - +
293B ASN* 1.3 55.2 + - - +
294B LYS 3.2 1.6 - - - -
295B SER* 2.8 23.0 + - - -
345B ASN* 3.8 20.2 - - - +
346B GLU* 4.4 11.4 - - + +
347B LEU* 3.9 10.9 + - - +
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Residues in contact with ASN 293 (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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189B LEU* 5.1 2.6 - - - +
291B PRO* 3.0 27.2 + - - +
292B GLU* 1.3 76.7 - - - +
294B LYS* 1.3 76.2 + - - +
295B SER 3.7 0.7 - - - -
296B PHE* 3.4 16.2 - - - -
347B LEU* 3.5 21.6 - - + +
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Residues in contact with LYS 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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189B LEU 3.9 10.5 - - - +
190B GLN* 3.0 27.0 + - - +
191B ILE* 4.9 1.6 - - - +
192B SER* 4.7 2.2 + - - +
195B ASP* 2.7 30.3 + - - +
290B ARG* 4.3 25.1 - - + +
291B PRO* 2.7 16.7 + - + +
293B ASN* 1.3 95.7 + - - +
295B SER* 1.3 61.3 + - - +
296B PHE* 3.3 14.6 - - + -
297B LEU* 3.2 33.5 + - + +
298B TYR* 4.2 7.9 - - - -
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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
----------------------------------------------------------
285B TRP* 3.4 31.6 - - - -
291B PRO 3.8 1.0 + - - -
292B GLU 2.8 18.0 + - - -
293B ASN 3.7 0.6 - - - -
294B LYS* 1.3 71.1 - - - +
296B PHE* 1.3 65.0 + - - +
297B LEU 3.0 4.1 + - - -
298B TYR* 3.0 21.1 + - - +
299B GLU* 4.0 7.0 + - - +
346B GLU* 3.2 24.4 - - - +
347B LEU 2.7 20.8 + - - -
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Residues in contact with PHE 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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182B LEU* 4.6 8.5 - - + -
189B LEU* 3.9 38.8 - - + -
191B ILE* 3.8 20.2 - - + -
293B ASN 3.4 23.3 - - - -
294B LYS* 4.1 12.3 - - + -
295B SER* 1.3 76.2 - - - +
297B LEU* 1.3 82.5 + - + +
299B GLU* 3.1 34.0 + - - +
300B ILE* 4.1 2.3 - - + +
340B VAL* 3.6 28.7 - - + -
347B LEU* 3.2 24.6 + - + +
348B ARG* 4.3 1.8 - - - -
349B ILE* 3.8 26.0 - - + +
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Residues in contact with LEU 297 (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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179B VAL* 3.8 28.3 - - + -
191B ILE* 4.6 4.9 - - + -
195B ASP* 4.1 28.5 - - + +
199B VAL* 4.5 7.7 - - + +
267B PHE* 3.9 30.5 - - + -
271B GLN* 4.0 13.7 - - - +
290B ARG* 4.7 1.8 - - + -
294B LYS* 3.5 30.5 - - + +
295B SER 3.0 1.6 + - - -
296B PHE* 1.3 104.1 - - + +
298B TYR* 1.3 61.2 + - - +
299B GLU 3.4 0.5 + - - -
300B ILE* 3.7 21.8 + - + +
301B VAL 5.0 0.5 + - - -
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Residues in contact with TYR 298 (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 PHE* 3.5 22.4 - + - -
270B GLU* 2.6 33.4 + - + -
271B GLN* 4.1 27.0 - - + +
285B TRP* 4.1 7.9 - + - -
287B TYR* 3.5 58.2 - + + +
290B ARG* 3.3 35.0 + - + -
294B LYS 4.2 6.5 - - - -
295B SER* 3.0 20.1 + - - +
297B LEU* 1.3 78.0 - - - +
299B GLU* 1.3 59.9 + - + +
300B ILE 3.3 1.6 + - - -
301B VAL 4.7 1.0 + - - -
302B SER 3.3 22.7 + - - +
303B ASN* 4.4 0.7 - - - -
304B LYS* 5.2 0.9 + - - +
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Residues in contact with GLU 299 (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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295B SER 4.7 4.5 - - - +
296B PHE* 3.1 17.0 + - - +
298B TYR* 1.3 77.6 - - + +
300B ILE* 1.3 63.0 + - - +
301B VAL 3.9 0.2 - - - -
303B ASN* 3.5 47.7 + - - +
304B LYS 5.8 0.7 - - - +
305B ARG* 3.2 39.9 + - + +
306B ASN* 5.2 0.4 + - - -
308B ILE 3.7 5.7 - - - +
309B ASP* 4.4 0.2 - - - -
346B GLU* 5.7 0.2 - - - +
348B ARG* 3.6 14.0 + - - -
349B ILE* 2.9 43.8 + - + +
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Residues in contact with ILE 300 (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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175B ALA* 3.8 33.2 - - + +
178B LEU* 4.0 19.7 - - + -
179B VAL* 3.9 35.0 - - + +
182B LEU* 5.1 4.3 - - + -
199B VAL* 3.9 13.7 - - + -
296B PHE 4.1 6.1 - - - +
297B LEU* 3.9 28.0 - - + +
298B TYR 3.3 2.4 - - - -
299B GLU* 1.3 78.0 - - - +
301B VAL* 1.3 64.1 + - + +
309B ASP* 3.3 4.9 - - - +
310B VAL* 3.0 36.6 + - + +
349B ILE* 4.2 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