Contacts of the helix formed by residues 291 - 302 (chain A) in PDB entry 6VSU
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A LEU* 3.3 8.6 - - - +
278A PHE* 3.5 26.6 - - - -
289A GLY 4.1 0.2 + - - -
290A LEU* 1.3 75.9 - - - +
292A PHE* 1.3 63.9 + - - +
293A ARG* 3.3 9.8 + - - +
294A ASP* 2.8 53.4 + - - +
295A VAL* 3.3 9.2 + - - +
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Residues in contact with PHE 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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274A LEU* 3.5 25.7 - - + +
278A PHE* 4.1 14.5 - - + -
291A SER* 1.3 72.8 - - - +
293A ARG* 1.3 57.1 + - - +
295A VAL* 3.4 4.7 + - - +
296A LEU* 3.1 49.4 + - + +
328A VAL* 3.5 35.2 - - + -
331A LYS* 3.9 19.5 - - + -
332A LEU* 3.8 27.1 - - + -
275C ASP* 4.0 7.2 - - - +
287C PRO* 3.7 20.4 - - + -
288C GLY* 3.4 32.5 - - - +
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 2.6 44.3 + - - -
291A SER* 3.3 8.3 + - - +
292A PHE* 1.3 74.1 - - - +
294A ASP* 1.4 56.1 + - - +
296A LEU* 3.4 21.2 - - - +
297A ASN* 2.8 57.6 + - - +
300A HIS* 4.4 2.4 + - - -
223C ARG* 3.9 2.8 - - - +
243C MET* 3.3 42.3 - - + +
244C ARG* 3.9 13.5 - - - +
246C PHE* 5.5 4.5 - - + -
275C ASP* 5.2 0.4 + - - -
288C GLY* 2.8 42.9 + - - +
289C GLY 4.6 7.0 - - - +
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Residues in contact with ASP 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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243A MET* 5.8 0.2 - - - +
246A PHE* 4.2 9.3 - - + -
250A ARG* 2.9 36.2 + - - -
254A GLU* 4.4 1.8 - - - +
289A GLY 5.0 0.5 - - - +
290A LEU* 3.7 21.8 - - + +
291A SER* 2.8 47.1 + - - +
292A PHE 3.3 0.2 - - - -
293A ARG* 1.4 73.3 - - - +
295A VAL* 1.3 65.8 - - - +
297A ASN* 3.2 10.9 + - - +
298A ILE* 3.1 27.4 + - - +
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Residues in contact with VAL 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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184A LEU* 4.3 16.4 - - + -
269A ILE* 5.0 0.9 - - + -
273A CYS* 4.0 19.5 - - - -
274A LEU* 3.7 17.9 - - + -
290A LEU* 4.1 14.6 - - + -
291A SER 3.3 13.3 + - - +
292A PHE 3.6 7.2 - - - +
293A ARG 3.3 0.2 - - - -
294A ASP* 1.3 76.2 - - - +
296A LEU* 1.3 60.6 + - + +
298A ILE* 3.1 10.2 + - - +
299A LEU* 2.9 47.5 + - + +
332A LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 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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103A GLU* 3.6 21.1 - - - +
292A PHE* 3.1 45.9 + - + +
293A ARG* 3.2 40.6 + - - +
295A VAL* 1.3 77.7 - - - +
297A ASN* 1.3 55.4 + - - +
299A LEU* 4.3 15.3 - - + +
300A HIS* 2.8 49.7 + - + +
331A LYS* 4.3 3.6 - - - -
332A LEU* 4.9 4.7 - - + -
335A GLU* 3.9 27.4 - - + -
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Residues in contact with ASN 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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250A ARG* 4.5 5.5 - - - +
254A GLU* 3.1 36.1 + - - +
293A ARG* 2.8 41.9 + - - +
294A ASP* 3.2 5.3 + - - +
296A LEU* 1.3 77.6 - - - +
298A ILE* 1.3 61.3 + - - +
300A HIS* 5.0 2.2 + - - -
301A ASN* 2.6 37.8 + - - +
243C MET 4.8 0.9 - - - +
244C ARG* 4.6 9.7 - - - +
247C SER* 3.2 24.8 + - - -
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Residues in contact with ILE 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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182A LEU* 4.0 26.7 - - + -
184A LEU* 4.4 11.7 - - + -
220A VAL* 4.0 26.2 - - + -
246A PHE* 4.9 5.4 - - + -
253A LEU* 3.7 39.2 - - + +
254A GLU* 4.5 7.3 - - + +
256A LEU* 4.1 7.8 - - + +
290A LEU* 4.7 11.9 - - + -
294A ASP 3.1 17.4 + - - +
295A VAL* 3.1 8.7 + - - +
297A ASN* 1.3 78.3 - - - +
299A LEU* 1.3 58.1 + - + +
301A ASN* 3.8 0.7 - - - +
302A LEU* 3.0 31.4 + - - +
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Residues in contact with LEU 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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182A LEU* 4.5 8.3 - - + -
184A LEU* 4.4 11.4 - - + -
267A ILE* 4.2 35.4 - - + -
269A ILE* 4.2 13.0 - - + -
295A VAL* 2.9 38.0 + - + +
296A LEU* 4.0 16.6 - - + +
298A ILE* 1.3 75.3 - - + +
300A HIS* 1.3 61.4 + - + +
302A LEU* 3.3 5.6 + - + -
332A LEU* 4.6 4.7 - - + -
335A GLU* 5.2 8.5 - - + -
336A LEU* 4.5 15.0 - - + +
339A LYS* 2.5 42.2 + - + -
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Residues in contact with HIS 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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103A GLU* 3.5 30.5 + - + -
104A GLU* 3.9 32.2 + - - +
293A ARG* 4.5 1.6 + - - -
296A LEU* 2.8 36.0 + - + +
297A ASN* 4.5 2.7 + - - +
299A LEU* 1.3 77.4 - - + +
301A ASN* 1.3 64.0 + - - +
302A LEU 3.9 0.3 + - - +
335A GLU* 2.8 36.6 + - + +
339A LYS* 3.9 9.8 + - + +
244C ARG* 3.8 22.6 + - + +
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Residues in contact with ASN 301 (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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254A GLU* 3.0 31.7 + - - +
255A ASN* 4.6 6.9 - - - +
256A LEU 3.7 10.2 + - - +
297A ASN* 2.6 36.0 + - - +
298A ILE 3.8 0.4 - - - -
299A LEU 3.3 0.2 - - - -
300A HIS* 1.3 79.3 - - - +
302A LEU* 1.3 64.6 + - - +
303A GLN* 3.1 7.4 + - - +
244C ARG 6.0 0.2 + - - -
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Residues in contact with LEU 302 (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* 4.0 17.5 - - + -
256A LEU* 3.6 33.2 - - + -
257A LYS 4.2 0.7 - - - +
258A LEU* 4.1 15.0 - - + -
265A VAL* 4.5 5.2 - - + -
267A ILE* 3.7 31.9 - - + -
298A ILE* 3.0 19.2 + - + +
299A LEU* 3.3 11.0 + - + +
300A HIS 4.5 0.5 - - - +
301A ASN* 1.3 75.8 - - - +
303A GLN* 1.3 71.7 + - - +
304A ALA* 3.7 17.6 + - + +
339A LYS* 2.5 33.1 + - - -
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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