Contacts of the helix formed by residues 291 - 300 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A TRP* 3.5 12.4 - - + +
290A ARG* 1.4 95.7 - - + +
292A GLU* 1.3 56.3 + - - +
293A ASN* 3.2 20.4 - - - +
294A LYS* 2.7 38.0 + - + -
295A SER 3.7 0.2 + - - -
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LEU* 5.2 9.4 - - - +
285A TRP* 3.6 53.6 + - + +
291A PRO* 1.3 72.5 - - - +
293A ASN* 1.3 56.5 + - - +
294A LYS 3.2 2.0 - - - -
295A SER* 2.8 23.5 + - - -
345A ASN* 3.7 21.5 - - - +
346A GLU* 4.3 8.5 - - + +
347A LEU 3.8 10.4 + - - -
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Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 5.0 3.1 - - - +
291A PRO* 3.0 26.6 + - - +
292A GLU* 1.3 77.2 - - - +
294A LYS* 1.3 73.1 + - - +
295A SER 3.7 0.4 - - - -
296A PHE* 3.3 17.0 - - - -
347A LEU* 3.5 23.7 - - + +
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU 3.9 10.3 - - - +
190A GLN* 2.9 26.8 + - - +
191A ILE* 4.8 1.8 - - - +
192A SER* 4.9 2.4 + - - -
195A ASP* 2.7 31.4 + - - +
290A ARG* 4.3 25.7 - - + +
291A PRO* 2.7 16.3 + - + +
293A ASN* 1.3 95.4 + - - +
295A SER* 1.3 60.4 + - - -
296A PHE* 3.3 16.8 - - + -
297A LEU* 3.2 31.2 + - + +
298A TYR* 4.3 7.4 - - - -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A TRP* 3.4 32.1 - - - -
291A PRO 3.7 1.2 + - - -
292A GLU 2.8 16.7 + - - -
293A ASN 3.7 0.8 - - - -
294A LYS* 1.3 70.7 - - - +
296A PHE* 1.3 63.2 + - - +
297A LEU 3.0 4.7 + - - -
298A TYR* 3.0 22.1 + - - +
299A GLU* 4.0 7.5 + - - +
346A GLU* 3.1 23.8 - - - +
347A LEU 2.7 20.9 + - - -
348A ARG* 5.8 0.2 - - - -
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU* 4.4 9.4 - - + -
189A LEU* 3.9 36.1 - - + -
191A ILE* 3.7 23.8 - - + -
293A ASN 3.3 24.2 - - - -
294A LYS* 3.9 14.8 - - + -
295A SER* 1.3 75.6 - - - +
297A LEU* 1.3 80.9 + - + +
299A GLU* 3.0 34.4 + - - +
300A ILE* 4.1 2.7 - - + +
340A VAL* 4.0 20.2 - - + -
347A LEU* 3.1 32.4 + - + +
348A ARG* 4.3 0.4 - - - -
349A ILE* 3.8 24.7 - - + +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.8 28.5 - - + -
191A ILE* 4.8 4.3 - - + -
195A ASP* 4.1 27.6 - - + +
199A VAL* 4.2 8.9 - - + +
267A PHE* 3.8 29.6 - - + -
271A GLN* 4.0 13.8 - - - +
290A ARG* 4.7 2.2 - - + -
294A LYS* 3.2 29.1 + - + +
295A SER 3.0 1.6 + - - -
296A PHE* 1.3 102.0 - - + +
298A TYR* 1.3 60.9 + - - +
299A GLU 3.2 1.3 + - - -
300A ILE* 3.6 22.2 + - + +
301A VAL 5.0 0.5 + - - -
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Residues in contact with TYR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 3.5 21.1 - + - -
270A GLU* 2.6 34.3 + - + -
271A GLN* 4.1 26.2 - - + +
285A TRP* 4.0 12.1 - + - -
287A TYR* 3.5 57.0 - + + +
290A ARG* 3.3 32.7 + - + -
294A LYS 4.3 3.1 - - - -
295A SER* 3.0 22.7 + - - +
297A LEU* 1.3 77.5 - - - +
299A GLU* 1.3 60.8 + - + +
300A ILE 3.3 1.6 + - - -
301A VAL 4.8 0.8 + - - -
302A SER 3.2 22.2 + - - +
303A ASN* 4.4 0.7 - - - -
304A LYS* 5.2 1.0 + - - +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 5.4 1.0 - - - +
295A SER 4.6 4.7 - - - +
296A PHE* 3.0 16.9 + - - +
298A TYR* 1.3 77.7 - - + +
300A ILE* 1.3 63.2 + - - +
301A VAL 3.9 0.2 - - - -
303A ASN* 3.5 47.4 + - - +
304A LYS 5.8 0.2 - - - +
305A ARG* 3.2 39.0 + - + +
306A ASN* 5.3 0.4 + - - -
308A ILE 3.7 5.9 - - - +
309A ASP* 4.5 0.2 - - - -
346A GLU* 5.6 0.3 - - - +
348A ARG* 3.6 13.6 + - - -
349A ILE* 2.9 45.2 + - + +
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA* 3.8 32.5 - - + +
178A LEU* 4.0 19.5 - - + -
179A VAL* 3.9 35.9 - - + +
182A LEU* 5.1 4.0 - - + -
199A VAL* 3.9 16.8 - - + -
296A PHE 4.1 7.2 - - - +
297A LEU* 3.6 26.9 + - + +
298A TYR 3.3 2.4 - - - -
299A GLU* 1.3 80.1 - - - +
301A VAL* 1.3 63.7 + - + +
309A ASP* 3.3 4.7 - - - +
310A VAL* 3.0 35.7 + - + +
349A ILE* 4.3 5.2 - - + -
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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