Contacts of the strand formed by residues 246 - 253 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A GLU* 5.0 14.3 + - - -
258A ARG* 6.1 0.2 - - - +
222L GLY* 4.2 3.8 + - - -
223L LEU* 3.6 28.5 - - + +
244L ARG 3.7 1.6 + - - -
245L SER* 1.3 68.3 - - - +
247L ALA* 1.3 62.3 + - - +
248L VAL* 5.6 5.6 - - + -
260L VAL 4.0 0.2 - - - +
261L VAL* 3.5 3.0 - - - -
262L THR* 3.0 37.9 + - - +
263L GLU* 2.9 53.2 + - + +
485L ARG 5.2 2.2 + - - -
487L GLU* 2.9 46.2 + - - +
489L GLN* 5.8 0.4 - - - +
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Residues in contact with ALA 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLU* 4.4 10.9 - - - +
251A GLU* 5.2 2.1 + - - +
245L SER* 3.4 5.6 + - - +
246L ARG* 1.3 75.4 - - - +
248L VAL* 1.3 69.3 + - - +
259L ILE* 4.3 3.4 - - + -
260L VAL 3.2 9.9 - - - +
261L VAL* 3.9 18.4 - - + -
318L LEU* 3.9 24.2 - - + +
322L TYR* 3.9 19.3 + - + +
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Residues in contact with VAL 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL* 3.8 39.9 - - + -
249A ILE 3.6 9.2 - - - +
250A GLU* 4.1 15.5 - - + +
246L ARG* 5.6 6.7 - - + -
247L ALA* 1.3 80.1 - - - +
249L ILE* 1.3 64.4 + - - +
250L GLU* 4.3 8.7 + - + +
259L ILE* 3.3 5.1 - - - +
260L VAL* 2.8 50.2 + - + +
262L THR* 6.4 1.3 - - + -
318L LEU* 5.6 1.3 - - - -
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Residues in contact with ILE 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL* 3.5 4.7 - - - +
249A ILE* 3.1 52.3 + - + +
257A GLN* 4.3 7.2 - - - +
315A SER* 4.9 0.7 - - - +
248L VAL* 1.3 74.9 - - - +
250L GLU* 1.3 64.8 + - - +
257L GLN* 4.0 23.6 - - + +
258L ARG 3.4 8.5 - - - +
259L ILE* 4.2 11.2 - - + -
314L ALA* 3.6 26.5 - - + +
315L SER* 3.4 41.5 - - - +
318L LEU* 4.6 14.6 - - + -
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Residues in contact with GLU 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ARG* 4.7 14.3 + - - +
247A ALA 4.6 7.4 - - - +
248A VAL* 4.2 22.4 - - + +
248L VAL* 4.4 5.3 - - + +
249L ILE* 1.3 75.7 - - - +
251L GLU* 1.3 66.5 - - - +
257L GLN* 3.4 5.4 - - - -
258L ARG* 2.9 78.1 + - + +
260L VAL* 3.5 18.5 - - + +
303L ARG* 3.9 6.4 + - - -
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Residues in contact with GLU 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LEU* 5.4 3.3 - - + +
244A ARG* 4.7 18.4 - - - +
247A ALA 5.2 2.2 + - - -
318A LEU* 6.2 4.8 - - + +
322A TYR* 5.6 6.3 - - + +
489A GLN* 3.4 18.4 + - - +
250L GLU* 1.3 83.0 - - - +
252L ARG* 1.3 58.3 + - - +
253L GLY* 3.6 6.5 - - - +
255L GLY* 6.3 2.0 - - - -
256L ARG 3.9 6.5 - - - +
257L GLN* 4.4 6.2 - - - +
258L ARG* 4.7 1.6 + - - -
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Residues in contact with ARG 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A GLN* 3.4 17.4 - - - +
490A LEU 4.4 7.4 - - - +
250L GLU 3.8 0.2 + - - -
251L GLU* 1.3 71.8 - - - +
253L GLY* 1.3 61.4 + - - +
256L ARG* 2.9 32.0 + - - +
257L GLN 2.5 29.6 + - - +
258L ARG* 4.1 29.2 - - + +
290L THR* 4.0 7.9 + - - +
293L ARG* 6.2 0.2 - - - +
307L ASP* 3.1 49.2 + - - +
308L VAL 3.5 13.7 + - - +
309L ARG* 5.5 0.8 - - - +
310L LYS 5.8 0.2 - - - +
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Residues in contact with GLY 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU* 5.7 5.2 - - - -
244A ARG* 6.2 1.8 - - - -
489A GLN* 3.2 16.5 + - - -
490A LEU 4.6 3.4 - - - -
491A GLY* 4.0 11.7 - - - -
251L GLU* 3.6 4.7 - - - +
252L ARG* 1.3 84.0 - - - +
254L GLY* 1.3 62.9 + - - -
255L GLY 3.2 3.1 - - - -
256L ARG* 3.4 17.6 + - - +
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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