Contacts of the helix formed by residues 348 - 361 (chain F) in PDB entry 1F9E
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 TRP 348 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340F TYR* 2.9 57.0 + + + +
342F ASN* 5.3 1.8 - - + -
346F GLY 4.9 3.8 - - - -
347F THR* 1.3 71.9 - - - +
349F TYR* 1.3 64.9 + - - +
351F GLN* 4.2 2.2 - - - +
352F SER* 3.1 27.2 + - - -
377F VAL* 3.9 9.8 - - + +
381F LYS* 3.4 95.6 - - + +
383F GLY 4.6 0.2 - - - -
385F GLN* 3.6 38.1 - - + +
4301S ASP* 3.1 38.3 + - - -
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Residues in contact with TYR 349 (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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281E PHE* 3.8 9.0 - + + -
282E ILE 4.3 5.2 - - - -
283E GLN* 3.2 17.3 - - + +
330F GLY* 3.4 38.4 + - - -
331F MET 3.6 11.9 + - - -
332F ALA* 3.3 30.1 - - + -
347F THR* 3.1 0.8 - - - -
348F TRP* 1.3 81.0 - - - +
350F ILE* 1.3 72.2 + - + +
352F SER* 3.5 2.1 - - - -
353F LEU* 2.7 44.3 + - + +
370F LEU* 3.5 21.3 - - + +
373F VAL* 3.7 25.4 - - + -
377F VAL* 4.6 3.4 - - - -
385F GLN* 3.7 10.5 - - - +
387F PRO* 4.1 14.8 - - + -
389F PRO* 5.8 1.5 - - + +
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Residues in contact with ILE 350 (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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185E ASP* 3.3 33.9 - - + +
189E LEU* 3.8 27.6 - - + -
233E CYS* 5.9 0.2 - - + -
235E LEU* 4.1 12.1 - - + -
281E PHE* 4.9 8.5 - - + -
283E GLN* 3.7 26.9 - - + +
347F THR* 3.1 19.4 + - - +
349F TYR* 1.3 86.0 - - + +
351F GLN* 1.3 65.3 + - - +
353F LEU* 2.9 20.9 + - + +
354F CYS* 2.9 26.5 + - - -
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Residues in contact with GLN 351 (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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184E LEU* 3.6 23.4 + - - +
185E ASP* 3.2 21.2 + - - +
188E ALA* 3.9 14.1 - - - +
345F GLU* 2.9 30.7 + - + +
346F GLY* 4.0 1.5 - - - -
347F THR 3.1 20.0 + - - +
348F TRP* 4.2 2.5 - - - +
350F ILE* 1.3 77.5 - - - +
352F SER* 1.3 58.8 + - - +
354F CYS* 3.3 4.6 + - - +
355F GLN* 2.9 46.7 + - - +
358F ARG* 5.4 4.0 + - - -
381F LYS* 6.4 1.3 - - - -
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Residues in contact with SER 352 (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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348F TRP 3.1 19.0 + - - -
349F TYR 3.5 2.5 - - - -
351F GLN* 1.3 77.7 - - - +
353F LEU* 1.3 55.6 + - - +
355F GLN* 3.3 15.4 + - - +
356F SER* 2.8 39.1 + - - -
373F VAL* 3.6 22.3 - - - +
376F GLU* 3.8 23.7 - - - +
377F VAL* 4.1 6.2 - - - +
381F LYS* 5.3 5.8 - - - -
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Residues in contact with LEU 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LEU* 4.9 7.4 - - + -
281E PHE* 3.4 53.4 - - + -
349F TYR* 2.7 24.8 + - + +
350F ILE* 2.9 23.3 + - + +
352F SER* 1.3 72.5 - - - +
354F CYS* 1.3 54.1 + - - +
356F SER* 3.4 1.7 + - - -
357F LEU* 2.8 63.4 + - + +
366F ILE* 5.4 1.1 - - + -
369F ILE* 4.9 4.0 - - + -
370F LEU* 4.5 14.4 - - + -
373F VAL* 4.2 16.3 - - + +
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Residues in contact with CYS 354 (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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188E ALA* 3.6 29.4 - - + -
189E LEU* 3.7 23.6 - - - -
192E THR* 3.4 26.7 - - - +
350F ILE* 2.9 20.4 + - - +
351F GLN* 3.7 7.2 - - - +
353F LEU* 1.3 71.4 - - - +
355F GLN* 1.3 66.4 + - - +
357F LEU* 3.0 9.2 + - - +
358F ARG* 2.8 41.0 + - - +
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Residues in contact with GLN 355 (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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351F GLN* 2.9 42.5 + - + +
352F SER* 3.5 16.2 - - - +
354F CYS* 1.3 74.6 - - - +
356F SER* 1.3 65.8 + - - +
358F ARG* 3.2 21.0 + - - +
359F GLU* 3.2 22.8 + - - +
381F LYS* 5.6 7.5 - - - +
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Residues in contact with SER 356 (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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352F SER* 2.8 21.7 + - - -
353F LEU 3.7 3.1 - - - -
355F GLN* 1.3 73.9 - - - +
357F LEU* 1.3 63.2 + - - +
359F GLU* 3.4 5.7 + - - +
360F ARG* 2.9 31.8 + - - +
369F ILE* 3.3 25.8 + - - +
372F GLU* 2.8 31.0 + - - +
373F VAL* 4.2 10.3 - - - -
376F GLU* 6.5 0.4 - - - -
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Residues in contact with LEU 357 (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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192E THR* 3.8 18.2 - - + -
193E PHE* 3.7 28.5 - - + -
196E LEU* 4.6 2.9 - - + +
281E PHE* 5.2 1.6 - - + -
353F LEU* 2.8 53.8 + - + +
354F CYS* 3.0 5.6 + - - +
356F SER* 1.3 72.9 - - - +
358F ARG* 1.3 63.5 + - - +
360F ARG* 4.7 0.2 - - - -
361F CYS* 3.0 57.6 + - - +
366F ILE* 5.1 4.7 - - + -
369F ILE* 3.9 20.2 - - + -
400F PHE* 4.4 14.1 - - + -
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Residues in contact with ARG 358 (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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188E ALA* 4.8 11.0 - - - +
191E THR* 4.3 17.9 - - - +
192E THR* 3.8 27.3 + - + +
195E GLU* 3.8 30.4 + - - +
351F GLN* 5.4 3.6 + - - -
354F CYS* 2.8 33.0 + - - +
355F GLN* 3.7 14.6 - - - +
357F LEU* 1.3 74.9 - - - +
359F GLU* 1.3 57.0 + - - +
362F PRO* 2.9 25.4 - - - +
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Residues in contact with GLU 359 (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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355F GLN* 3.2 21.1 + - - +
356F SER* 3.5 9.6 - - - +
358F ARG* 1.3 75.6 - - - +
360F ARG* 1.3 63.3 + - + +
362F PRO* 3.0 42.1 + - - +
372F GLU* 3.7 18.4 - - - +
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Residues in contact with ARG 360 (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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356F SER* 2.9 26.7 + - - +
359F GLU* 1.3 79.5 - - + +
361F CYS* 1.3 56.9 + - - +
362F ARG* 2.7 53.6 + - - +
363F GLY 3.2 7.1 + - - -
364F ASP* 2.8 47.0 + - + +
368F THR* 3.8 13.3 - - - +
369F ILE* 3.7 22.0 - - + -
372F GLU* 2.4 44.1 + - - +
149G LEU 4.9 3.0 + - - -
150G ASP* 2.7 39.0 + - - +
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Residues in contact with CYS 361 (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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196E LEU* 4.0 15.7 - - + -
357F LEU* 3.0 47.1 + - - +
360F ARG* 1.3 73.4 - - - +
362F PRO* 1.3 66.3 - - + +
363F GLY* 2.7 22.2 + - - +
364F ASP 4.5 8.7 - - - -
369F ILE* 3.9 9.6 - - - +
399F VAL* 5.2 0.2 - - - +
400F PHE* 3.4 45.0 - - - +
401F PRO* 4.7 5.9 - - - +
402F SER* 4.8 1.0 + - - -
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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