Contacts of the strand formed by residues 313 - 317 (chain X) in PDB entry 6JM9
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 TYR 313 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243X PHE* 5.7 3.7 - + - -
267X VAL* 3.6 6.2 - - - +
268X SER 2.8 26.2 + - - +
269X SER* 3.8 11.9 - - - -
270X LYS 3.6 21.5 - - - +
271X PRO* 3.6 44.7 - - + +
275X LEU* 3.9 18.6 - - + -
293X VAL* 5.0 0.4 - - + -
294X VAL 3.7 5.8 - - - +
295X GLU* 3.2 44.7 + - + -
296X LEU* 4.3 2.0 - - - +
311X SER* 4.3 16.0 - - - -
312X TYR* 1.3 75.0 - - - +
314X LEU* 1.4 59.7 + - - +
315X HIS* 3.3 23.9 - - + +
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Residues in contact with LEU 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X GLU* 6.3 0.4 - - + -
151X ILE* 3.8 35.0 - - + -
265X ARG* 4.4 14.8 - - + -
266X ILE 3.9 7.2 - - - +
267X VAL* 5.0 3.4 - - + +
292X ARG 4.0 0.5 - - - +
293X VAL* 3.7 1.9 - - - -
294X VAL* 2.9 45.2 + - + +
296X LEU* 3.9 25.7 - - + +
313X TYR* 1.4 56.6 - - - +
315X HIS* 1.4 73.4 + - - +
316X THR* 3.9 15.3 + - - +
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Residues in contact with HIS 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265X ARG* 3.5 3.3 - - - -
266X ILE* 2.9 43.6 + - + +
268X SER* 3.4 17.3 - - - -
270X LYS 3.4 10.3 + - - -
271X PRO* 4.2 0.7 - - + -
272X PHE* 3.3 37.9 - + + -
273X ALA 4.2 0.9 - - - -
291X MET* 3.5 24.6 - - + -
292X ARG 3.2 7.0 - - - +
293X VAL* 3.3 35.4 - - + +
313X TYR* 3.3 24.2 - - - +
314X LEU* 1.4 77.9 - - - +
316X THR* 1.4 61.4 + - - +
317X ILE 4.3 0.2 - - - -
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Residues in contact with THR 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263X GLY* 4.6 5.2 - - - +
264X GLY 3.7 8.5 - - - +
265X ARG* 4.3 13.4 - - + +
291X MET* 3.3 3.7 - - - -
292X ARG* 2.9 37.5 + - - +
314X LEU* 3.9 19.9 - - - +
315X HIS* 1.4 73.0 + - - +
317X ILE* 1.4 73.2 + - - +
318X ASP* 3.3 14.5 + - - +
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Residues in contact with ILE 317 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257X PHE 4.4 6.1 - - - +
260X MET* 4.6 9.0 - - + +
261X LYS 4.0 6.7 - - - +
262X GLU* 3.7 24.6 - - + +
263X GLY* 3.4 24.2 + - - +
264X GLY* 2.9 27.1 + - - +
266X ILE* 3.7 16.6 - - + -
290X ILE* 3.4 32.3 - - + +
291X MET* 3.7 27.4 - - + -
316X THR* 1.4 71.9 - - - +
318X ASP* 1.4 67.6 + - - +
319X ARG* 3.8 18.4 - - - +
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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