Contacts of the helix formed by residues 370 - 388 (chain A) in PDB entry 4RPP
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 TYR 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A MET* 3.9 14.0 + - + +
336A LYS 3.3 24.8 + - - -
337A LYS* 3.2 23.6 - - - +
338A PRO* 3.8 25.2 - - + +
364A GLU 3.9 4.5 - - - +
368A GLY 3.3 0.4 - - - -
369A ASP* 1.3 98.7 - - + +
371A PRO* 1.3 63.6 - - - +
372A LEU 3.3 2.2 - - - -
373A GLU* 3.4 35.4 - - + +
374A ALA* 3.4 19.2 + - - +
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Residues in contact with PRO 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 4.0 24.5 - - + +
55A SER* 4.5 5.8 - - - -
60A THR* 4.7 9.6 - - + -
64A MET* 5.0 3.6 - - + -
364A GLU 3.4 12.5 - - - +
365A THR* 3.5 45.7 - - - +
368A GLY 3.7 6.5 - - - +
369A ASP 3.4 9.9 - - - +
370A TYR* 1.3 89.4 - - - +
372A LEU* 1.3 65.0 + - + +
373A GLU* 4.8 0.4 - - - +
374A ALA 3.5 7.3 + - - -
375A VAL* 3.5 7.8 - - - +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 4.6 4.9 - - + +
63A GLU* 3.6 39.5 - - + +
64A MET* 3.7 16.4 - - + +
67A SER* 3.3 22.0 - - - +
370A TYR 3.3 0.2 - - - -
371A PRO* 1.3 82.1 - - + +
373A GLU* 1.3 75.2 + - - +
375A VAL* 3.5 4.4 + - + +
376A ARG* 3.3 51.7 + - - +
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A MET* 3.5 16.8 - - + +
338A PRO* 3.8 15.0 - - + +
339A ARG* 6.1 1.1 - - - +
370A TYR* 3.4 40.1 - - + +
371A PRO* 3.4 0.9 - - - +
372A LEU* 1.3 84.6 + - - +
374A ALA* 1.3 59.5 + - - +
376A ARG* 3.5 12.1 + - - +
377A MET* 3.0 33.0 + - + +
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.9 3.7 - - + +
334A MET* 3.6 22.0 - - + +
361A LEU* 3.8 12.4 - - + +
364A GLU* 4.0 27.6 - - + +
365A THR* 4.2 1.8 - - + -
370A TYR 3.4 11.3 + - - +
371A PRO 3.6 10.5 - - - +
372A LEU 3.2 0.6 - - - -
373A GLU* 1.3 79.4 - - - +
375A VAL* 1.3 56.4 + - - +
377A MET* 3.4 1.7 + - - +
378A GLN* 2.9 29.6 + - - +
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 4.2 9.9 - - + +
49A CYS* 3.5 25.6 - - - -
64A MET* 3.9 15.5 - - + +
67A SER* 3.7 31.6 - - - +
68A GLY 4.3 2.2 - - - -
69A MET 3.9 15.9 - - - +
361A LEU* 4.1 5.6 - - + -
365A THR* 3.9 8.1 - - + -
371A PRO 3.5 14.8 - - - +
372A LEU* 3.5 7.1 + - - +
373A GLU 3.3 0.4 - - - -
374A ALA* 1.3 73.5 - - - +
376A ARG* 1.3 59.8 + - - +
378A GLN* 3.2 3.3 + - - +
379A HIS* 2.8 28.2 + - - +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.5 22.6 + - - -
67A SER* 3.2 27.8 + - - +
372A LEU* 3.3 36.6 + - - +
373A GLU* 3.9 11.0 - - - +
375A VAL* 1.3 77.7 - - - +
377A MET* 1.3 57.8 + - + +
379A HIS* 3.5 9.5 - - - +
380A LEU* 3.1 34.5 + - + +
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LEU* 4.5 1.8 - - + -
334A MET* 4.0 9.2 - - + -
339A ARG* 3.6 42.0 - - - +
340A PRO* 3.6 29.6 - - + -
373A GLU 3.0 19.3 + - - +
374A ALA 3.7 3.4 - - - +
376A ARG* 1.3 75.4 - - + +
378A GLN* 1.3 66.3 + - - +
380A LEU* 3.1 18.5 + - + +
381A ILE* 3.0 46.4 + - + +
303B ALA* 4.9 6.3 - - + +
304B GLU* 4.3 17.3 - - - +
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.9 18.6 - - + -
330A MET* 3.6 19.4 - - - +
331A LEU* 4.1 5.5 - - - +
348A VAL* 3.1 30.2 - - - +
359A ILE* 3.6 33.3 - - + +
360A MET 4.4 1.4 + - - -
361A LEU* 3.3 32.6 - - + +
374A ALA 2.9 18.1 + - - +
375A VAL* 3.4 9.2 - - - +
377A MET* 1.3 76.0 - - - +
379A HIS* 1.3 61.9 + - - +
381A ILE* 4.1 1.8 - - - +
382A ALA* 3.1 27.0 + - - +
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Residues in contact with HIS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 3.0 45.5 + - + +
47A ILE* 3.8 10.5 - - + +
67A SER 3.9 17.7 + - - +
68A GLY* 5.8 0.7 - - - -
375A VAL 2.8 17.0 + - - +
376A ARG* 3.5 8.5 - - - +
378A GLN* 1.3 77.3 - - - +
380A LEU* 1.3 71.1 - - + +
382A ALA* 3.9 0.7 - - - +
383A ARG* 3.0 64.1 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 3.1 16.8 + - + +
377A MET* 3.1 24.9 + - + +
379A HIS* 1.3 90.5 - - + +
381A ILE* 1.3 63.2 + - - +
383A ARG* 3.4 7.5 + - + +
384A GLU* 3.0 33.1 + - + +
304B GLU* 3.8 30.5 - - + +
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LEU* 4.6 11.4 - - + -
340A PRO* 5.0 2.0 - - + -
345A GLY* 3.3 42.4 - - - +
348A VAL* 3.7 20.4 - - + -
349A ALA* 3.9 12.9 - - + +
377A MET* 3.0 42.3 + - + +
378A GLN* 4.1 3.8 - - - +
380A LEU* 1.3 73.3 - - - +
382A ALA* 1.3 59.2 + - - +
384A GLU* 3.3 4.2 + - - +
385A ALA* 2.9 27.5 + - - +
303B ALA 4.6 2.9 - - - +
304B GLU* 4.0 26.5 - - + -
307B PHE* 4.9 3.9 - - + -
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.8 21.3 - - - -
45A THR* 4.0 13.0 - - - +
348A VAL* 4.9 0.6 - - - +
352A VAL* 4.4 7.7 - - + +
359A ILE* 4.0 17.3 - - + -
378A GLN 3.1 19.1 + - - +
381A ILE* 1.3 78.2 - - - +
383A ARG* 1.3 62.1 + - - +
385A ALA* 3.2 8.5 + - - +
386A GLU* 3.2 29.3 + - - +
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 3.9 38.8 + - + +
40A ILE* 5.3 0.6 - - - +
41A THR* 2.8 34.6 + - - +
42A ALA* 4.5 7.6 - - - +
43A ARG* 4.4 14.7 - - + +
379A HIS* 3.0 47.8 + - - +
380A LEU* 3.8 7.9 - - + +
382A ALA* 1.3 75.9 - - - +
384A GLU* 1.3 63.3 + - + +
386A GLU* 3.3 23.7 - - - +
387A ALA 4.1 0.9 + - - -
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Residues in contact with GLU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER 5.2 1.6 - - - +
39A PRO* 3.2 30.3 - - + +
380A LEU* 3.0 24.0 + - + +
381A ILE* 3.5 5.4 - - - +
383A ARG* 1.3 77.7 - - - +
385A ALA* 1.3 61.5 + - - +
386A GLU 3.1 0.2 - - - -
387A ALA* 3.0 25.5 + - - +
388A ALA 3.9 1.7 + - - -
304B GLU* 4.0 30.0 - - + +
305B LYS* 3.1 34.5 + - - -
307B PHE* 4.6 6.3 - - + -
308B LEU* 3.6 24.0 - - + +
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ALA* 3.9 24.0 - - - +
352A VAL* 3.8 20.0 - - + -
353A LEU* 3.5 7.0 - - + +
381A ILE 2.9 17.5 + - - +
382A ALA* 3.2 7.4 + - - +
384A GLU* 1.3 75.5 - - - +
386A GLU* 1.3 61.7 + - - +
387A ALA 3.2 0.2 - - - -
388A ALA 3.2 10.2 + - - +
389A ILE* 3.3 15.6 + - - +
307B PHE* 3.8 16.5 - - + -
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.3 13.5 - - - +
42A ALA 4.4 5.8 - - - +
43A ARG* 3.8 6.1 - - - -
44A ASN* 3.1 49.3 + - - +
45A THR* 3.4 9.4 + - - -
352A VAL* 3.4 15.8 - - - +
382A ALA 3.2 20.5 + - - +
383A ARG* 3.3 13.5 - - - +
384A GLU 3.1 0.4 - - - -
385A ALA* 1.3 78.0 - - - +
387A ALA* 1.3 61.9 + - - +
389A ILE* 3.2 43.5 + - + +
391A HIS* 3.8 16.4 - - + +
467A ARG* 4.3 3.7 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.7 14.7 + - - -
33A LEU* 4.2 9.9 - - + +
39A PRO* 5.5 11.2 - - + -
41A THR* 5.5 1.4 + - - -
383A ARG 4.1 1.9 + - - +
384A GLU* 3.0 17.4 + - - +
386A GLU* 1.3 79.7 - - - +
388A ALA* 1.3 57.0 + - - +
389A ILE 3.1 6.8 + - - +
391A HIS* 5.5 1.0 - - - -
308B LEU* 5.5 5.6 - - + -
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 5.5 0.3 - - - -
29A HIS* 3.3 9.8 + - - -
30A MET* 3.7 18.2 - - + +
33A LEU* 3.9 19.7 - - + +
353A LEU* 3.7 23.5 - - + +
384A GLU 3.9 0.6 + - - -
385A ALA 3.2 12.6 + - - +
387A ALA* 1.3 77.5 - - - +
389A ILE* 1.3 60.7 + - - +
390A TYR 3.5 1.7 + - - -
307B PHE* 4.5 3.4 - - + -
308B LEU* 3.7 24.9 - - + -
311B LYS* 5.3 0.9 - - + -
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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
------------------------------------------------------------
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