Contacts of the strand formed by residues 329 - 340 (chain F) in PDB entry 6Q2J
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 PHE 329 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F VAL* 4.7 3.6 - - + -
293F VAL* 4.1 18.2 - - + -
318F LEU* 4.0 11.7 - - + +
324F TRP* 5.2 4.9 - + - -
325F ALA* 2.7 21.9 + - + +
326F GLN* 4.0 14.8 - - - +
328F THR* 1.3 101.6 - - - +
330F ARG* 1.3 61.7 + - - +
356F LEU* 4.5 22.9 - - + -
357F VAL 3.5 11.2 - - - -
358F LEU* 3.6 25.4 - - + -
359F ASN* 5.0 3.3 + - - -
362F LEU* 5.0 1.3 - - + -
370F MET* 3.8 34.3 - - + -
372F LEU* 4.4 15.3 - - + -
395F VAL* 4.0 23.1 - - + -
397F VAL* 5.0 5.4 - - + -
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Residues in contact with ARG 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F GLU 4.6 2.8 + - - -
290F ASP* 4.0 12.7 + - - +
318F LEU* 5.0 1.3 - - - -
329F PHE* 1.3 76.1 - - - +
331F VAL* 1.3 66.3 - - - +
332F GLU* 3.6 17.1 + - - +
356F LEU* 3.6 4.5 - - - -
357F VAL* 2.9 63.0 + - + +
358F LEU 3.5 15.0 + - - -
359F ASN* 3.5 29.9 + - - +
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Residues in contact with VAL 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F SER* 4.4 15.4 + - - +
318F LEU* 3.7 43.7 - - + +
330F ARG* 1.3 76.5 - - - +
332F GLU* 1.3 60.4 + - - +
333F HIS 3.8 1.9 + - - -
354F TYR* 4.5 18.2 - - + -
355F ARG 3.4 11.2 - - - +
356F LEU* 3.8 15.5 - - + -
374F VAL* 3.8 29.4 - - + -
393F PHE* 5.6 1.3 - - + -
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Residues in contact with GLU 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F ARG* 3.6 20.6 + - + +
331F VAL* 1.3 72.3 - - - +
333F HIS* 1.3 61.5 + - - +
334F TRP* 3.2 35.3 + - + -
353F ASP 4.1 0.5 - - - +
354F TYR* 3.7 1.4 - - - -
355F ARG* 2.9 47.8 + - + +
357F VAL* 3.4 25.0 - - + +
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Residues in contact with HIS 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F LEU* 4.4 7.2 - - + +
314F TYR* 4.2 26.8 - - + +
316F SER* 4.1 12.8 - - - +
331F VAL 3.8 2.5 + - - +
332F GLU* 1.3 76.3 - - - +
334F TRP* 1.3 83.4 + - - +
335F PRO* 4.0 10.2 - - + +
352F HIS* 3.6 28.6 + + + -
353F ASP 3.4 8.5 + - - -
354F TYR* 3.2 48.1 + + + -
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Residues in contact with TRP 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F GLU* 3.2 46.7 - - + -
333F HIS* 1.3 81.9 - - - +
335F PRO* 1.3 80.8 - - + +
353F ASP* 2.9 48.4 + - + +
355F ARG* 3.3 48.2 - - - +
702F NAG 4.5 18.4 + - + +
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Residues in contact with PRO 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F SER* 6.2 0.7 - - - +
310F LEU* 3.6 42.2 - - + -
333F HIS* 4.0 4.9 - - + +
334F TRP* 1.3 102.9 - - + +
336F ASN* 1.3 68.2 + - - +
350F THR* 5.6 2.0 - - + -
351F VAL 3.5 7.4 - - - +
352F HIS* 3.5 28.5 - - + +
353F ASP* 5.9 0.4 - - - -
702F NAG 4.0 8.8 - - - +
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Residues in contact with ASN 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D ARG* 4.1 6.4 + - - -
335F PRO* 1.3 76.6 - - - +
337F GLU* 1.3 75.7 + - - +
338F THR* 6.1 1.0 - - - -
350F THR* 3.3 9.2 - - - +
351F VAL* 2.9 37.7 + - + +
353F ASP* 5.7 4.0 - - - +
702F NAG 1.4 73.6 + - - +
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Residues in contact with GLU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D ARG* 3.2 31.8 + - + +
295D THR* 4.9 2.6 - - - -
296D ILE 5.3 1.7 - - - +
303F VAL* 3.8 27.1 - - - +
336F ASN* 1.3 91.1 + - - +
338F THR* 1.3 62.4 + - - +
348F ARG* 2.9 38.9 + - + +
349F ALA 3.2 14.4 - - - +
350F THR* 4.1 13.1 - - + +
351F VAL 4.6 0.7 - - - +
702F NAG 5.0 2.1 + - - +
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Residues in contact with THR 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297F ARG* 6.1 0.2 - - - +
299F PHE* 5.6 4.7 - - + -
336F ASN* 6.1 0.9 - - - -
337F GLU* 1.3 75.2 - - - +
339F SER* 1.3 76.1 + - - +
340F VAL* 6.3 0.7 - - + -
348F ARG* 3.3 10.7 - - - +
349F ALA* 2.9 33.6 + - + +
351F VAL* 3.9 27.6 - - + -
702F NAG 4.6 14.2 + - - -
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Residues in contact with SER 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F THR* 1.3 92.5 + - - +
340F VAL* 1.3 60.3 + - - +
346F PHE* 3.9 34.8 - - - -
347F VAL 3.8 4.0 - - - -
348F ARG* 4.4 7.4 - - - +
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Residues in contact with VAL 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F PHE* 4.6 28.5 - - + -
301F ALA* 6.6 0.2 - - + -
338F THR* 4.3 1.2 + - + -
339F SER* 1.3 75.1 - - - +
341F GLN* 1.3 77.4 + - - +
346F PHE* 3.4 4.5 - - - -
347F VAL* 2.9 49.6 + - + +
349F ALA* 4.7 8.3 - - + -
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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