Contacts of the strand formed by residues 246 - 253 (chain R) in PDB entry 6QX2
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 ARG 246 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222R GLY* 4.2 4.2 + - - -
223R LEU* 3.6 28.3 - - + +
244R ARG 3.7 1.4 + - - -
245R SER* 1.3 68.2 - - - +
247R ALA* 1.3 62.2 + - - +
248R VAL* 5.5 7.0 - - + -
260R VAL 4.0 0.2 - - - +
261R VAL* 3.5 2.5 - - - -
262R THR* 3.0 38.1 + - - +
263R GLU* 2.9 52.9 + - + +
485R ARG 5.3 2.4 + - - -
487R GLU* 2.9 45.8 + - - +
489R GLN* 5.6 1.0 - - - +
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Residues in contact with ALA 247 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245R SER* 3.4 6.5 + - - +
246R ARG* 1.3 73.9 - - - +
248R VAL* 1.3 68.1 + - - +
259R ILE* 4.3 4.0 - - + -
260R VAL 3.2 10.3 - - - +
261R VAL* 3.9 18.6 - - + -
318R LEU* 4.0 24.4 - - + +
322R TYR* 3.9 19.4 + - + +
327R LEU* 5.3 0.2 - - + -
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Residues in contact with VAL 248 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246R ARG* 5.5 7.2 - - + -
247R ALA* 1.3 79.7 - - - +
249R ILE* 1.3 71.8 + - - +
250R GLU* 4.3 12.5 + - + +
258R ARG 3.9 0.2 - - - +
259R ILE* 3.3 6.2 - - - +
260R VAL* 2.8 48.7 + - + +
262R THR* 6.3 2.0 - - + -
318R LEU* 5.6 1.3 - - - -
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Residues in contact with ILE 249 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248R VAL* 1.3 77.8 - - - +
250R GLU* 1.3 65.5 + - - +
257R GLN* 3.9 24.2 - - + +
258R ARG 3.4 8.1 - - - +
259R ILE* 4.3 11.7 - - + -
314R ALA* 3.6 26.7 - - + +
315R SER* 3.4 41.7 - - - +
318R LEU* 4.5 15.0 - - + -
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Residues in contact with GLU 250 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248R VAL* 4.7 11.1 - - + +
249R ILE* 1.3 75.0 - - - +
251R GLU* 1.3 80.2 + - + +
257R GLN* 3.4 6.9 - - - -
258R ARG* 2.9 38.0 + - + +
260R VAL* 3.1 35.7 - - + +
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Residues in contact with GLU 251 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250R GLU* 1.3 95.3 - - + +
252R ARG* 1.3 65.9 + - - +
253R GLY 5.3 0.4 - - - +
255R GLY* 6.6 0.2 - - - -
256R ARG 3.9 6.1 - - - -
257R GLN* 4.6 5.0 - - - +
258R ARG* 5.7 0.6 - - - +
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Residues in contact with ARG 252 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250R GLU 3.8 0.4 + - - -
251R GLU* 1.3 80.3 - - - +
253R GLY* 1.3 60.0 + - - +
256R ARG* 2.9 46.6 + - - +
257R GLN 2.9 20.4 + - - +
258R ARG* 3.9 6.5 - - + -
290R THR* 4.0 11.3 + - - +
293R ARG* 6.0 1.6 - - - +
307R ASP* 3.4 35.6 + - - +
308R VAL 2.8 39.8 + - - +
309R ARG* 5.8 0.8 - - - +
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Residues in contact with GLY 253 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251R GLU* 5.3 0.6 - - - +
252R ARG* 1.3 82.8 + - - +
254R GLY* 1.3 62.8 + - - -
255R GLY 3.2 2.9 - - - -
256R ARG* 3.1 31.2 + - - +
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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