Contacts of the helix formed by residues 292 - 300 (chain B) in PDB entry 6Y2G
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 THR 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLY 3.4 26.7 - - - +
110B GLN* 4.2 3.6 - - + -
111B THR* 4.1 18.6 - - + +
203B ASN* 3.4 5.8 - - - +
206B ALA* 4.1 2.2 - - - -
291B PHE* 1.3 74.6 - - - +
293B PRO* 1.3 73.7 - - - +
294B PHE* 3.5 16.1 + - + +
295B ASP* 2.9 35.9 + - - +
296B VAL* 3.0 21.8 + - - +
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Residues in contact with PRO 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.3 12.3 - - + +
203B ASN* 3.8 9.9 - - - +
206B ALA* 3.8 13.9 - - + -
249B ILE* 3.7 38.4 - - + +
250B LEU* 4.0 23.8 - - + -
253B LEU* 4.7 5.6 - - + +
292B THR* 1.3 89.3 - - - +
294B PHE* 1.3 66.7 + - + +
296B VAL* 3.1 7.0 + - + +
297B VAL* 3.1 28.0 + - + +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 6.3 1.1 - - - -
249B ILE* 3.8 38.4 - - + -
292B THR* 3.9 17.0 - - + +
293B PRO* 1.3 77.0 - - + +
295B ASP* 1.3 58.6 + - - +
297B VAL* 3.8 5.9 - - - +
298B ARG* 2.7 39.4 + - + +
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Residues in contact with ASP 295 (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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3B PHE* 5.0 2.0 - - - -
8B PHE* 5.9 1.7 - - - -
111B THR* 2.8 31.7 + - - +
127B GLN* 4.3 8.2 + - - +
290B GLU 4.1 1.4 - - - +
291B PHE* 3.7 18.0 - - + -
292B THR* 2.9 40.1 + - - +
294B PHE* 1.3 78.1 - - - +
296B VAL* 1.3 60.8 + - - +
298B ARG* 3.8 26.0 + - - +
299B GLN* 3.3 28.5 + - - +
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Residues in contact with VAL 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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3B PHE* 4.0 20.6 - - + -
206B ALA* 3.6 32.1 - - + +
207B TRP* 4.4 0.4 - - - +
210B ALA* 3.7 26.7 - - + +
213B ILE* 5.0 4.3 - - + -
253B LEU* 4.1 18.4 - - + -
291B PHE* 4.3 9.4 - - + -
292B THR 3.0 18.0 + - - +
293B PRO 3.1 8.0 + - - +
295B ASP* 1.3 77.2 - - - +
297B VAL* 1.3 57.9 - - - +
299B GLN* 4.2 0.5 - - - +
300B CYS* 3.1 32.8 + - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO* 4.9 9.6 - - + -
253B LEU* 3.6 31.6 - - + -
293B PRO 3.1 16.6 + - - +
294B PHE* 3.8 6.3 - - - +
296B VAL* 1.3 75.1 - - - +
298B ARG* 1.4 66.7 + - - +
299B GLN 3.0 3.5 + - - -
300B CYS* 3.2 9.5 + - - +
301B SER* 3.0 27.6 + - - -
303B VAL* 6.5 0.2 - - + -
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Residues in contact with ARG 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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123A SER 3.6 22.8 + - - -
124A GLY* 4.4 0.4 - - - -
6B MET* 3.4 34.2 + - - +
7B ALA 3.8 24.0 + - - -
8B PHE* 3.8 32.1 - - + +
127B GLN* 4.2 13.7 - - - +
294B PHE 2.7 22.0 + - - +
295B ASP* 3.8 24.3 + - - +
297B VAL* 1.4 73.8 - - - +
299B GLN* 1.3 61.0 + - - +
301B SER* 4.2 0.4 - - - -
302B GLY* 3.5 18.4 + - - -
303B VAL* 3.5 32.5 + - + -
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Residues in contact with GLN 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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139A SER* 2.9 27.3 + - - +
141A LEU* 3.4 18.9 - - - +
2B GLY 5.0 1.1 - - - +
3B PHE* 3.3 31.1 - - + -
4B ARG 2.7 46.5 + - - +
6B MET* 3.6 24.7 - - + +
291B PHE* 4.4 4.0 - - - -
295B ASP* 3.3 15.7 + - - +
297B VAL 3.0 0.6 - - - -
298B ARG* 1.3 81.2 - - + +
300B CYS* 1.3 60.1 + - - +
301B SER 3.2 4.9 - - - -
302B GLY* 4.4 1.5 + - - +
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Residues in contact with CYS 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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141A LEU* 3.8 14.4 - - + -
2B GLY 5.6 2.7 - - - -
3B PHE* 4.3 19.1 - - - -
210B ALA* 5.3 1.1 - - - -
213B ILE* 4.5 28.5 - - + -
214B ASN* 4.7 6.5 - - - -
256B GLN* 5.6 4.2 - - - +
296B VAL* 3.1 26.2 + - - +
297B VAL* 3.2 6.6 + - - +
299B GLN* 1.3 76.9 - - - +
301B SER* 1.4 56.1 + - - -
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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