Contacts of the helix formed by residues 308 - 325 (chain T) in PDB entry 6FF7
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 SER 308 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271T GLU* 5.3 11.0 - - - -
304T LEU* 2.8 24.2 + - - +
307T VAL* 1.3 77.2 - - - +
309T PRO* 1.3 66.0 - - - +
310T ARG 3.2 3.1 - - - -
311T GLY* 3.1 17.9 + - - +
312T ILE* 3.1 10.2 + - - +
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Residues in contact with PRO 309 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304T LEU 4.3 0.7 - - - +
305T THR* 3.6 24.2 - - - +
306T GLN 5.1 0.4 - - - +
307T VAL 4.1 0.4 - - - -
308T SER* 1.3 74.6 - - - +
310T ARG* 1.3 57.5 + - - +
312T ILE* 3.6 2.7 + - + +
313T ASN* 3.0 28.6 + - - +
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Residues in contact with ARG 310 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308T SER 3.2 0.8 - - - -
309T PRO* 1.3 76.4 - - - +
311T GLY* 1.3 60.9 + - - +
313T ASN* 3.4 8.7 + - - +
314T ALA* 3.0 27.9 + - - +
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Residues in contact with GLY 311 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275T LEU* 5.8 9.1 - - - +
308T SER* 3.1 15.1 + - - -
310T ARG* 1.3 78.9 - - - +
312T ILE* 1.3 62.1 + - - +
314T ALA* 3.1 10.9 + - - +
315T ILE* 3.1 18.9 + - - +
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Residues in contact with ILE 312 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301T GLY* 5.3 1.8 - - - +
304T LEU* 4.2 26.4 - - + +
305T THR* 4.7 6.3 - - - +
308T SER* 3.1 14.1 + - - +
309T PRO 4.2 3.1 - - - +
311T GLY* 1.3 74.2 - - - +
313T ASN* 1.3 56.2 + - - +
315T ILE* 3.1 11.0 + - + +
316T PHE* 2.9 28.4 + - - +
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Residues in contact with ASN 313 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309T PRO 3.0 19.0 + - - +
310T ARG* 3.5 9.6 - - - +
312T ILE* 1.3 77.0 - - - +
314T ALA* 1.3 56.6 + - - +
316T PHE* 3.3 6.9 + - - +
317T GLU* 2.9 30.0 + - - +
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Residues in contact with ALA 314 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310T ARG 3.0 13.8 + - - +
311T GLY* 3.3 11.9 - - - +
313T ASN* 1.3 72.2 - - - +
315T ILE* 1.3 66.8 + - - +
317T GLU* 3.4 6.4 + - - +
318T ARG* 3.0 24.1 + - - +
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Residues in contact with ILE 315 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278T LEU* 5.2 14.4 - - + -
311T GLY 3.1 11.9 + - - +
312T ILE* 3.1 12.7 + - - +
314T ALA* 1.3 76.1 - - - +
316T PHE* 1.3 57.1 - - - +
318T ARG* 3.1 9.4 + - - +
319T LEU* 2.9 27.6 + - - +
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Residues in contact with PHE 316 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312T ILE 2.9 14.7 + - - +
313T ASN* 3.3 6.9 + - - +
315T ILE* 1.3 73.4 - - - +
317T GLU* 1.3 61.2 + - - +
319T LEU* 3.4 8.7 + - - +
320T ARG* 2.9 27.9 + - - +
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Residues in contact with GLU 317 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313T ASN 2.9 17.6 + - - +
314T ALA* 3.6 8.1 - - - +
316T PHE* 1.3 75.9 - - - +
318T ARG* 1.3 56.5 + - - +
320T ARG* 3.1 8.1 + - - +
321T ASN* 2.9 28.2 + - - +
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Residues in contact with ARG 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282T LEU* 5.3 14.6 - - + -
314T ALA 3.0 13.9 + - - +
315T ILE* 3.3 11.4 - - - +
317T GLU* 1.3 76.5 - - - +
319T LEU* 1.3 62.9 + - - +
321T ASN* 3.2 9.3 + - - +
322T ILE* 3.0 21.7 + - - +
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Residues in contact with LEU 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282T LEU* 6.2 0.8 - - - +
315T ILE 2.9 12.6 + - - +
316T PHE* 3.6 11.9 - - - +
318T ARG* 1.3 74.8 - - - +
320T ARG* 1.3 57.5 + - - +
322T ILE* 3.2 8.7 + - - +
323T LEU* 2.8 28.2 + - - +
336T ILE* 5.0 15.5 - - + +
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Residues in contact with ARG 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ILE* 2.5 24.8 - - - +
316T PHE 2.9 14.7 + - - +
317T GLU* 3.1 8.9 + - - +
319T LEU* 1.3 76.5 - - - +
321T ASN* 1.3 54.6 + - - +
323T LEU* 3.5 7.6 - - + +
324T HIS* 3.0 9.9 + - - +
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Residues in contact with ASN 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A SER* 3.2 0.6 + - - -
317T GLU 2.9 12.8 + - - +
318T ARG* 3.2 11.2 + - - +
320T ARG* 1.3 75.9 - - - +
322T ILE* 1.3 58.0 + - - +
324T HIS* 5.3 0.4 - - - -
325T GLU* 2.6 50.1 + - + +
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Residues in contact with ILE 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ILE* 0.9 82.3 - - - +
360A SER* 1.2 38.4 + - - -
282T LEU 6.2 0.4 - - - +
285T PRO* 5.2 12.3 - - + -
318T ARG 3.0 12.2 + - - +
319T LEU* 3.5 11.4 - - - +
321T ASN* 1.3 70.2 - - - +
323T LEU 1.3 47.9 - - - +
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Residues in contact with LEU 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LEU* 6.1 1.1 - - + +
357A ASN* 3.0 20.9 - - - +
358A PRO* 1.7 21.6 - - + +
359A ILE* 0.9 256.8 + - + +
319T LEU 2.8 16.2 + - - +
320T ARG* 3.5 8.1 - - + +
322T ILE* 1.3 44.9 - - - +
324T HIS* 1.3 39.5 + - + -
336T ILE* 4.8 14.4 - - + -
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Residues in contact with HIS 324 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASN* 5.3 5.4 - - + +
358A PRO 4.1 0.6 - - - +
359A ILE* 1.7 18.2 - - - +
360A SER 3.4 0.7 - - - -
362A ARG* 5.8 1.6 - - - +
272B THR 5.1 2.9 - - - +
276B TYR* 3.2 36.3 - - + -
320T ARG 3.7 8.7 - - - +
321T ASN* 5.3 0.4 - - - -
323T LEU* 1.3 69.8 - - + +
325T GLU* 1.3 57.9 + - + +
326T SER 3.0 15.1 + - - +
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Residues in contact with GLU 325 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A SER* 3.2 2.2 - - - -
272B THR* 6.1 5.2 - - - -
321T ASN* 2.6 30.2 + - + +
324T HIS* 1.3 72.6 - - + +
326T SER* 1.3 57.2 + - - +
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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