Contacts of the helix formed by residues 307 - 329 (chain F) in PDB entry 6VVT
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 PRO 307 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 3.5 26.2 - - + +
305F ARG* 4.1 9.2 - - - +
306F ILE* 1.3 88.5 - - + +
308F VAL* 1.3 67.8 + - + +
309F HIS* 3.1 22.7 - - + +
310F MET* 2.9 13.4 + - + -
311F VAL 2.9 10.6 + - - -
21O T 3.8 28.3 - - + +
22O G 3.2 27.6 - - + +
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Residues in contact with VAL 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ARG* 3.6 31.4 - - - +
298F ALA* 4.2 13.0 - - + -
299F ASP* 3.3 25.4 - - - +
306F ILE 3.5 0.2 + - - -
307F PRO* 1.3 71.6 - - + +
309F HIS* 1.3 60.7 + - + +
311F VAL* 3.2 9.6 + - - +
312F GLU* 2.5 39.8 + - - +
22O G 4.8 6.0 + - + +
23O T 3.6 36.1 - - + +
2P G 5.9 0.2 - - - +
3P C 5.3 4.9 - - - +
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Residues in contact with HIS 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F PRO* 3.1 24.8 - - + +
308F VAL* 1.3 86.5 - - + +
310F MET* 1.3 79.3 + - + +
312F GLU* 3.2 15.2 - - - +
313F VAL* 3.0 27.7 + - - +
20O T 3.9 6.5 - - + +
21O T 2.9 72.2 + + + +
22O G 5.3 5.4 - - - +
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Residues in contact with MET 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 3.6 25.6 - - + +
37D ARG* 6.4 0.2 - - - -
306F ILE* 3.2 20.9 - - + -
307F PRO* 2.9 5.8 + - + +
309F HIS* 1.3 92.9 - - + +
311F VAL* 1.3 59.9 + - - +
312F GLU 3.0 1.3 - - - -
313F VAL* 2.9 23.2 - - + +
314F ILE* 2.9 41.9 + - + +
347F LYS* 4.8 14.8 - - - +
351F ILE* 4.4 16.4 - - + -
354F TYR* 4.0 32.1 - - + -
20O T 5.9 1.8 - - - +
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Residues in contact with VAL 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F ALA* 3.8 35.4 - - + +
302F ARG* 5.0 11.4 - - - +
306F ILE* 3.2 41.5 - - + +
307F PRO 2.9 3.1 + - - +
308F VAL 3.6 5.6 - - - +
310F MET* 1.3 75.9 - - - +
312F GLU* 1.3 60.6 + - - +
314F ILE* 4.0 8.0 - - + +
315F ASN* 2.9 47.6 + - - +
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Residues in contact with GLU 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F VAL* 2.5 22.8 + - - +
309F HIS* 3.2 16.9 - - - +
311F VAL* 1.3 75.3 - - - +
313F VAL* 1.3 62.3 + - - +
315F ASN* 3.5 5.5 + - - +
316F LYS* 3.1 21.2 + - + +
1P A 5.6 1.3 + - - +
2P G 3.4 52.7 + - + +
3P C 3.6 31.8 + - - -
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Residues in contact with VAL 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F HIS* 3.0 16.8 + - - +
310F MET* 2.9 43.1 - - + +
312F GLU* 1.3 72.0 - - - +
314F ILE* 1.3 59.8 + - + +
316F LYS* 3.1 8.6 + - + +
317F LEU* 2.8 28.1 + - - +
341F MET* 3.5 16.6 - - + +
343F ILE* 5.5 1.3 - - + -
351F ILE* 3.7 26.2 - - + -
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Residues in contact with ILE 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F ARG* 4.6 9.9 - - - +
306F ILE* 4.2 22.2 - - + -
310F MET* 2.9 29.3 + - - +
311F VAL* 4.0 7.0 - - + +
313F VAL* 1.3 77.2 - - + +
315F ASN* 1.3 63.8 + - - +
317F LEU* 3.2 6.9 + - + +
318F GLY* 3.0 25.3 + - - -
351F ILE* 4.0 24.7 - - + -
354F TYR* 4.5 7.9 - - + -
355F ALA* 3.9 41.1 - - + +
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Residues in contact with ASN 315 (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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311F VAL* 2.9 36.8 + - - +
312F GLU* 3.9 4.8 - - - +
314F ILE* 1.3 81.8 - - - +
316F LYS* 1.3 58.5 + - - +
318F GLY* 3.4 2.8 + - - +
319F ARG* 2.9 28.8 + - - +
322F ARG* 5.3 0.7 + - - -
1P A 5.0 19.7 + - - +
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Residues in contact with LYS 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F GLU* 3.1 14.2 + - + +
313F VAL* 3.1 13.3 + - + +
315F ASN* 1.3 77.8 - - - +
317F LEU* 1.3 56.8 + - - +
319F ARG* 3.2 24.6 + - - +
320F ILE* 2.9 38.1 + - + +
341F MET* 3.5 30.8 + - + +
2P G 3.8 27.3 + - - +
3P C 5.3 6.1 + - - -
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Residues in contact with LEU 317 (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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313F VAL 2.8 19.8 + - - +
314F ILE* 3.6 9.0 - - + +
316F LYS* 1.3 70.8 - - - +
318F GLY* 1.3 56.1 + - - +
320F ILE* 3.1 2.9 + - - +
321F GLN* 2.7 44.9 + - - +
337F LEU* 3.8 27.5 - - + +
341F MET* 3.2 29.8 - - + +
343F ILE* 4.8 2.0 - - + -
348F VAL* 3.8 33.4 - - + -
351F ILE* 4.6 14.8 - - + -
352F GLN* 4.3 20.2 - - + +
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Residues in contact with GLY 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F ILE 3.0 13.8 + - - -
315F ASN* 3.8 2.9 - - - -
317F LEU* 1.3 78.7 - - - +
319F ARG* 1.3 57.0 + - - +
321F GLN* 3.5 15.2 - - - +
322F ARG* 2.8 52.5 + - - -
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Residues in contact with ARG 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F ASN 2.9 18.3 + - - +
316F LYS* 3.4 19.9 - - - +
317F LEU 3.1 0.2 - - - -
318F GLY* 1.3 73.6 - - - +
320F ILE* 1.3 80.4 + - - +
322F ARG* 3.3 15.1 + - - +
323F GLU* 2.8 57.5 + - + +
1P A 3.3 12.7 + - - -
2P G 2.1 37.3 + - - -
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Residues in contact with ILE 320 (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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316F LYS* 2.9 27.2 + - + +
317F LEU* 3.6 6.7 - - - +
319F ARG* 1.3 97.3 - - - +
321F GLN* 1.3 54.0 + - - +
323F GLU* 3.1 17.2 + - + +
324F LEU* 2.6 42.8 + - + +
337F LEU* 3.7 20.0 - - + +
340F GLU* 3.4 41.1 - - + +
341F MET* 4.7 11.9 - - + -
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Residues in contact with GLN 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F LEU* 2.7 24.7 + - - +
318F GLY* 3.5 13.5 - - - +
320F ILE* 1.3 71.8 - - - +
322F ARG* 1.3 52.3 + - - +
324F LEU* 3.5 0.7 - - - +
325F LEU* 2.6 43.6 + - + +
331F GLU* 6.0 3.2 - - + +
332F PRO* 4.1 21.1 + - + +
337F LEU* 3.8 24.0 - - + +
352F GLN* 3.8 23.4 - - - +
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Residues in contact with ARG 322 (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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410C ASN* 3.1 44.6 + - - +
411C ILE* 5.7 4.7 - - + +
412C ARG* 4.4 16.9 - - + +
315F ASN 5.3 0.6 + - - -
318F GLY* 2.8 50.5 + - - +
319F ARG* 3.3 19.6 - - - +
321F GLN* 1.3 73.2 + - - +
323F GLU* 1.3 62.9 + - + +
325F LEU* 3.5 14.0 - - + +
326F GLN* 3.1 23.2 + - - +
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Residues in contact with GLU 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F ARG* 2.8 52.1 + - + +
320F ILE* 3.6 16.0 - - + +
322F ARG* 1.3 75.7 - - + +
324F LEU* 1.3 65.7 + - - +
326F GLN* 3.0 16.9 + - - +
327F ASP* 3.0 22.8 + - - +
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Residues in contact with LEU 324 (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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320F ILE* 2.6 30.4 + - + +
323F GLU* 1.3 72.4 - - - +
325F LEU* 1.3 62.2 + - - +
327F ASP* 4.5 5.4 - - + +
328F LEU* 3.0 65.7 + - + +
330F ARG 4.2 0.5 - - - +
332F PRO* 3.6 26.7 - - + -
336F GLU* 3.8 17.9 - - + +
337F LEU* 4.1 6.1 - - + -
340F GLU* 3.8 35.2 - - + +
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Residues in contact with LEU 325 (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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144C PHE* 3.2 31.6 - - + -
146C GLY* 5.7 0.2 - - - -
147C ASP* 5.8 2.0 - - - +
411C ILE* 5.2 13.7 - - + -
415C VAL* 5.6 9.9 - - + -
321F GLN* 2.6 27.3 + - + +
322F ARG* 3.5 15.0 - - + +
324F LEU* 1.3 73.5 - - - +
326F GLN* 1.3 60.3 + - - +
329F GLY 3.2 15.9 + - - -
330F ARG 4.1 17.0 - - - -
331F GLU* 4.3 16.8 - - + +
332F PRO* 4.0 3.3 - - + +
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Residues in contact with GLN 326 (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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142C THR 5.4 2.3 - - - +
143C VAL* 2.9 21.4 - - - +
144C PHE* 2.4 61.2 + - - +
406C GLN* 4.6 27.6 - - + +
409C ILE* 4.7 8.1 + - - +
411C ILE* 3.4 24.4 - - - +
322F ARG 3.1 11.6 + - - +
323F GLU* 3.0 11.2 + - - +
325F LEU* 1.3 77.8 - - - +
327F ASP* 1.3 66.2 + - - +
329F GLY 4.4 0.2 - - - -
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Residues in contact with ASP 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLN* 5.6 4.9 - - - +
323F GLU* 3.0 21.5 + - - +
324F LEU* 4.0 3.7 - - + +
326F GLN* 1.3 86.4 - - - +
328F LEU* 1.3 74.9 + - + +
329F GLY 3.6 0.2 + - - -
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Residues in contact with LEU 328 (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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125C PHE* 5.8 1.0 - - - -
324F LEU* 3.0 42.9 + - + +
327F ASP* 1.3 86.5 - - + +
329F GLY* 1.3 60.3 + - - +
330F ARG* 3.4 19.3 + - + +
332F PRO* 5.0 0.7 - - + -
336F GLU* 2.9 39.0 - - - +
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Residues in contact with GLY 329 (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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107C LYS* 4.5 8.0 + - - -
123C PRO* 4.5 2.8 - - - +
125C PHE* 4.7 6.0 - - - -
144C PHE* 3.0 58.2 - - - -
147C ASP* 4.5 0.3 - - - +
325F LEU 3.2 6.5 + - - -
326F GLN 4.4 0.8 - - - -
327F ASP 3.4 3.0 + - - -
328F LEU* 1.3 77.3 - - - +
330F ARG* 1.3 59.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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