Contacts of the helix formed by residues 358 - 377 (chain B) in PDB entry 3IFS
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 THR 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B GLU* 4.1 21.5 + - + +
339B LEU 3.1 13.9 - - - +
340B THR* 4.0 13.7 - - - +
341B ILE* 3.9 2.6 - - - +
356B GLY 5.0 2.0 - - - +
357B GLU* 1.3 79.9 + - - +
359B VAL* 1.3 64.3 + - - +
360B ASP* 3.5 8.1 + - - +
361B PHE* 3.1 33.7 + - - +
362B VAL* 3.4 15.4 + - - +
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.6 33.2 - - + +
123A SER* 3.8 24.5 - - - +
126A MSE 4.2 10.5 - - + -
154A LEU* 4.5 7.0 - - + -
158A ILE* 4.0 21.8 - - + -
339B LEU* 2.9 33.6 + - + +
340B THR 5.5 0.2 - - - -
341B ILE* 4.3 12.8 - - + +
358B THR* 1.3 71.7 - - - +
360B ASP* 1.3 58.8 + - - +
362B VAL* 3.1 11.8 + - - +
363B ASN* 3.0 22.5 + - - +
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Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE 5.0 1.1 - - - +
123A SER* 4.4 7.9 + - - +
275B GLU* 4.5 5.4 - - - +
331B LYS* 5.5 1.8 + - - -
332B VAL 5.3 4.1 - - - +
333B GLY 4.6 8.3 - - - +
335B SER* 3.9 28.9 + - - -
338B GLU* 3.7 22.4 + - - +
358B THR* 3.2 3.8 + - - +
359B VAL* 1.3 79.2 - - - +
361B PHE* 1.3 60.0 + - - +
363B ASN* 3.2 17.9 + - - +
364B THR* 2.8 42.9 + - - -
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Residues in contact with PHE 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU 4.3 9.4 - - - -
433A LEU* 3.8 32.8 - - + -
354B LEU* 4.3 2.9 - - + -
357B GLU* 3.8 44.0 - - + +
358B THR* 3.1 26.8 + - - +
360B ASP* 1.3 74.1 - - - +
362B VAL* 1.3 62.9 + - + +
364B THR* 3.2 8.0 + - - -
365B LYS* 2.9 64.8 + - + +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.7 24.0 - - + -
150A THR* 4.3 20.0 - - + -
154A LEU* 4.3 8.1 - - + -
429A MSE 5.0 2.3 - - - +
433A LEU* 3.8 26.6 - - + +
341B ILE* 3.9 20.6 - - + -
354B LEU* 4.3 11.7 - - + -
358B THR 3.4 13.4 + - - +
359B VAL 3.1 8.6 + - - +
361B PHE* 1.3 81.7 - - + +
363B ASN* 1.3 62.1 + - - +
365B LYS* 3.3 2.9 + - - +
366B ALA* 3.0 21.0 + - - +
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Residues in contact with ASN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.2 46.4 + - - +
274B TYR* 3.0 49.4 + - - +
275B GLU* 4.0 12.5 + - - +
308B SER 4.9 2.6 + - - -
331B LYS* 5.9 0.2 - - - -
359B VAL 3.0 8.2 + - - +
360B ASP* 3.6 17.2 + - - +
362B VAL* 1.3 76.2 - - - +
364B THR* 1.3 58.0 + - - +
366B ALA* 3.3 4.8 + - - +
367B TYR* 3.0 28.4 + - - +
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Residues in contact with THR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LYS* 3.9 28.1 + - - +
360B ASP* 2.8 30.4 + - - -
361B PHE* 3.5 8.4 - - - -
363B ASN* 1.3 75.7 - - - +
365B LYS* 1.3 66.6 + - - +
367B TYR* 3.2 8.5 + - + +
368B GLU* 2.9 46.5 + - + +
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A MSE 4.1 6.8 - - - +
432A LEU* 3.9 34.4 - - + +
433A LEU* 3.6 34.8 - - + -
361B PHE* 2.9 47.6 + - + +
362B VAL 3.3 0.2 + - - -
364B THR* 1.3 80.0 - - - +
366B ALA* 1.3 61.3 + - - +
368B GLU* 2.8 32.2 + - - +
369B GLY* 2.9 27.7 + - - -
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Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.8 15.7 - - + -
425A TYR* 5.9 0.7 - - + -
429A MSE 3.7 29.5 - - - +
274B TYR* 4.2 11.0 - - + -
308B SER* 5.0 4.9 - - - -
311B LEU* 5.8 1.3 - - + -
362B VAL 3.0 12.8 + - - +
363B ASN* 3.5 9.6 - - - +
364B THR 3.3 0.2 - - - -
365B LYS* 1.3 76.2 - - - +
367B TYR* 1.3 57.2 + - - +
369B GLY* 4.0 0.2 - - - -
370B THR* 2.7 41.0 + - - +
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B TYR* 3.5 38.0 + + + -
329B VAL* 3.7 26.7 - - + -
331B LYS* 3.6 41.9 - - + +
363B ASN 3.0 14.1 + - - +
364B THR* 3.2 12.1 + - + +
366B ALA* 1.3 77.0 - - - +
368B GLU* 1.3 81.4 + - + +
370B THR* 3.8 1.2 - - - -
371B LEU* 3.0 44.1 + - + +
383B ILE* 3.0 38.7 - - + +
385B ASN* 4.9 0.5 + - - -
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 3.7 15.1 - - + +
449A LEU* 3.8 33.8 - - + +
364B THR* 2.9 26.3 + - - +
365B LYS* 2.8 38.5 + - - +
366B ALA 3.4 0.2 - - - -
367B TYR* 1.3 94.4 - - + +
369B GLY* 1.3 62.4 + - - +
371B LEU* 3.3 5.1 + - - +
372B LEU* 3.2 28.3 + - - +
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Residues in contact with GLY 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A TYR 4.5 3.4 - - - -
428A ASN* 3.2 33.7 + - - -
429A MSE 4.2 4.9 - - - -
432A LEU* 3.6 9.7 - - - +
365B LYS 2.9 16.3 + - - -
366B ALA 4.0 0.4 - - - -
368B GLU* 1.3 77.2 - - - +
370B THR* 1.3 56.1 + - - +
372B LEU* 3.5 2.1 + - - -
373B ALA* 3.0 25.8 + - - +
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Residues in contact with THR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A TYR* 3.4 25.0 + - + +
274B TYR* 3.4 18.2 - - - +
307B PHE* 4.4 2.0 - - + -
311B LEU* 3.5 24.3 - - + +
366B ALA 2.7 23.2 + - - -
367B TYR 3.8 0.2 - - - -
369B GLY* 1.3 74.8 - - - +
371B LEU* 1.3 60.3 + - - +
373B ALA 3.3 0.2 + - - -
374B HIS* 2.8 66.5 + - + +
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 5.7 2.0 - - + -
11B LYS* 3.9 25.6 - - + -
329B VAL* 4.9 3.6 - - + -
367B TYR* 3.0 33.0 + - + +
368B GLU* 3.3 5.1 + - - +
370B THR* 1.3 76.6 - - - +
372B LEU* 1.3 67.3 + - + +
374B HIS* 3.5 1.6 + - - +
375B SER* 2.7 46.2 + - - +
381B ASN* 3.7 35.8 + - + +
383B ILE* 3.7 34.1 - - + -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A ASN* 4.1 8.3 - - - +
432A LEU* 5.1 0.7 - - + -
445A LEU* 3.8 33.7 - - + +
448A ARG* 3.8 37.0 - - + +
449A LEU* 3.8 36.1 - - + -
11B LYS* 5.2 6.7 - - + -
368B GLU 3.2 16.3 + - - +
369B GLY 3.9 3.6 - - - +
371B LEU* 1.3 87.1 - - + +
373B ALA* 1.3 60.9 + - - +
375B SER* 3.7 3.8 - - - +
376B ASP* 2.9 35.9 + - - +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ALA* 3.8 8.1 - - + -
425A TYR* 3.6 29.8 - - + +
428A ASN* 3.4 11.8 - - - +
319B GLN* 3.0 20.3 + - - +
369B GLY 3.0 18.1 + - - +
370B THR 3.3 3.6 + - - +
372B LEU* 1.3 75.7 - - - +
374B HIS* 1.3 64.4 + - + +
376B ASP* 3.1 7.9 + - - +
377B GLY 2.9 17.8 + - - -
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Residues in contact with HIS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A TYR* 5.2 4.1 - - + +
307B PHE* 3.8 12.1 - + - -
311B LEU* 3.8 10.9 - - + +
315B GLY* 4.7 4.8 + - - -
318B VAL* 3.5 28.3 - - + +
319B GLN* 3.4 24.8 + - - +
327B GLU* 2.7 34.4 + - - +
370B THR* 2.8 49.3 + - + +
371B LEU* 4.0 0.4 - - - +
373B ALA* 1.3 75.7 - - + +
375B SER* 1.3 60.4 + - - +
377B GLY* 3.1 8.5 + - - +
378B GLY 3.3 0.5 + - - -
379B VAL* 2.9 30.7 + - + +
381B ASN* 3.7 10.1 + - - +
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG* 4.9 5.8 - - - -
11B LYS 4.1 12.5 + - - -
14B SER* 5.7 2.0 - - - -
15B PHE* 3.4 23.2 - - - -
371B LEU* 2.7 34.4 + - - +
372B LEU* 3.7 7.9 - - - -
373B ALA 3.3 0.2 - - - -
374B HIS* 1.3 75.4 - - - +
376B ASP* 1.3 62.5 + - - +
378B GLY* 3.0 16.3 + - - -
379B VAL 3.5 15.9 + - - -
381B ASN* 4.1 6.2 + - - +
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Residues in contact with ASP 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ASN* 5.3 2.9 + - - -
445A LEU* 5.7 0.2 - - - +
448A ARG* 3.0 40.7 + - - -
319B GLN* 4.7 1.6 - - - +
372B LEU 2.9 19.6 + - - +
373B ALA* 3.1 7.4 + - - +
375B SER* 1.3 78.9 - - - +
377B GLY* 1.3 56.3 + - - +
378B GLY 3.2 1.0 + - - -
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Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLN* 5.5 2.1 + - - -
319B GLN* 3.6 27.2 - - - +
323B ARG* 2.9 30.5 + - - -
373B ALA 2.9 9.9 + - - -
374B HIS* 3.1 6.0 + - - -
376B ASP* 1.3 75.2 - - - +
378B GLY* 1.3 56.7 + - - +
379B VAL 3.7 0.2 - - - -
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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
------------------------------------------------------------
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