Contacts of the helix formed by residues 360 - 376 (chain D) in PDB entry 3RMD
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 360 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357D SER* 3.1 12.9 + - - +
358D VAL 3.1 2.5 - - - -
359D PHE* 1.3 78.8 - - - +
361D PRO* 1.3 64.1 - - - +
362D ILE* 3.4 1.7 - - - +
363D LYS* 2.9 25.6 + - - +
364D THR* 2.9 24.3 + - - -
2K G 2.7 36.0 + - - -
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Residues in contact with PRO 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LYS* 4.8 14.4 - - - +
358D VAL 5.0 1.6 - - - +
359D PHE 3.3 12.6 - - - +
360D SER* 1.3 82.7 - - - +
362D ILE* 1.3 64.4 + - - +
364D THR* 3.2 7.1 + - - +
365D TRP* 2.8 30.0 + - + +
565D SER* 3.7 44.2 - - - +
568D GLY* 5.6 1.3 - - - -
569D ALA* 4.4 8.3 - - + +
2K G 3.2 19.5 - - - +
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Residues in contact with ILE 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D SER* 3.4 8.5 - - - +
361D PRO* 1.3 77.6 - - - +
363D LYS* 1.3 70.2 + - + +
366D ASP* 3.0 31.2 + - + +
569D ALA* 4.1 12.2 - - + +
572D ASN* 4.0 19.7 - - + +
574D TRP* 4.0 7.2 - - + +
575D PHE* 3.3 54.5 - - + +
576D ARG 4.9 0.2 - - - +
1K C 4.1 20.4 - - - +
2K G 3.1 19.5 + - - +
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Residues in contact with LYS 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ASP* 2.9 38.2 + - - +
90D LEU* 4.1 14.6 - - + +
353D ILE* 4.7 9.9 - - + -
357D SER* 3.8 27.6 - - - +
360D SER* 2.9 21.7 + - - +
362D ILE* 1.3 83.4 - - + +
364D THR* 1.3 68.8 + - - +
366D ASP* 3.2 15.0 + - - +
367D ALA* 3.1 21.1 + - - +
576D ARG* 5.9 0.2 - - - +
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Residues in contact with THR 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D MET* 4.0 13.8 - - + +
351D ALA* 4.0 7.7 - - + +
353D ILE* 3.8 15.2 - - + +
357D SER 3.3 12.7 + - - -
358D VAL* 4.1 8.5 + - - -
360D SER 2.9 20.2 + - - -
361D PRO* 3.6 7.3 - - - +
363D LYS* 1.3 78.7 - - - +
365D TRP* 1.3 65.4 + - + +
367D ALA* 3.3 3.1 + - - +
368D ILE* 3.0 32.4 + - + +
562D LEU* 3.7 30.1 - - + -
565D SER* 6.0 0.4 - - - -
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Residues in contact with TRP 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D PRO* 2.8 20.9 + - + +
364D THR* 1.3 72.5 - - + +
366D ASP* 1.3 66.0 + - - +
368D ILE* 4.1 17.7 - - + -
369D ILE* 3.0 47.7 + - + +
471D VAL 5.7 0.2 - - - -
474D GLU* 3.8 39.3 - - + -
475D ILE* 3.8 22.4 - - + -
478D VAL* 4.1 9.4 - - + -
562D LEU* 3.0 49.6 + - + +
565D SER* 3.6 13.2 + - - -
566D LEU* 3.2 41.4 - - + +
569D ALA* 4.7 3.4 - - + -
575D PHE* 4.4 17.0 - - + -
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Residues in contact with ASP 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D MET* 3.6 11.5 - - - +
90D LEU* 4.5 1.0 - - + +
362D ILE* 3.0 22.1 + - + +
363D LYS* 3.2 23.2 + - - +
365D TRP* 1.3 75.9 - - - +
367D ALA* 1.3 57.6 + - - +
369D ILE* 3.8 4.2 - - - +
370D PHE* 2.9 28.8 + - - +
575D PHE* 4.2 10.8 - - + -
576D ARG* 2.6 56.5 + - - +
577D TYR* 4.1 4.6 + - - -
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Residues in contact with ALA 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU* 4.0 17.7 - - + +
351D ALA 3.2 10.1 - - - +
352D LYS 4.5 0.7 - - - +
353D ILE* 3.2 35.2 - - + -
363D LYS 3.1 4.8 + - - +
364D THR 3.7 3.6 - - - +
366D ASP* 1.3 78.5 - - - +
368D ILE* 1.3 66.7 + - - +
370D PHE* 3.0 8.9 + - + -
371D ASN* 2.9 34.3 + - - +
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Residues in contact with ILE 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D TYR* 3.3 42.4 - - + +
351D ALA* 3.4 28.9 - - + +
364D THR* 3.0 18.4 + - + +
365D TRP* 3.8 28.9 - - + +
367D ALA* 1.3 75.6 - - - +
369D ILE* 1.3 59.6 + - - +
371D ASN* 4.2 3.7 - - - +
372D SER* 3.3 21.0 + - - -
474D GLU* 4.5 6.9 - - + +
478D VAL* 5.3 2.9 - - + -
562D LEU* 3.8 20.4 - - + -
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Residues in contact with ILE 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D TRP* 3.0 37.7 + - + +
366D ASP 3.8 1.6 - - - +
368D ILE* 1.3 74.8 - - - +
370D PHE* 1.3 68.0 + - - +
372D SER* 3.2 2.1 + - - -
373D LEU* 2.9 34.0 + - + +
470D VAL* 4.2 11.7 - - + -
471D VAL* 5.1 13.9 - - + -
474D GLU* 3.9 26.5 - - + -
566D LEU* 5.6 2.0 - - + -
575D PHE* 4.2 10.1 - - + -
577D TYR* 3.0 52.3 - - + +
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Residues in contact with PHE 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D MET* 3.5 55.9 - - + -
90D LEU* 3.8 15.7 - - + -
91D ALA* 3.8 7.9 - - + -
94D SER* 3.4 30.1 - - - -
95D ASP* 5.6 0.4 - - - -
366D ASP 2.9 19.4 + - - +
367D ALA* 3.3 9.0 - - + +
369D ILE* 1.3 77.9 - - - +
371D ASN* 1.3 56.1 + - - +
373D LEU* 3.1 2.1 + - - +
374D LYS* 2.8 59.7 + - + -
380D ILE* 3.9 22.7 - - + -
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Residues in contact with ASN 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU 5.5 0.4 + - - -
94D SER* 2.9 32.7 - - - +
351D ALA 3.5 10.1 + - - -
352D LYS* 3.4 40.9 + - + +
367D ALA* 2.9 25.7 + - - +
368D ILE* 4.2 4.4 - - - +
370D PHE* 1.3 77.2 - - - +
372D SER* 1.3 63.9 + - - +
374D LYS* 3.2 11.6 + - - +
375D GLU* 3.1 23.4 + - - +
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Residues in contact with SER 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D ILE 3.3 13.3 + - - -
369D ILE 3.2 4.5 + - - -
371D ASN* 1.3 79.8 - - - +
373D LEU* 1.3 60.9 + - - +
375D GLU* 3.5 13.4 + - - +
376D GLN* 3.0 27.9 + - - +
474D GLU* 2.4 42.1 + - - -
477D LYS* 4.0 11.7 + - - -
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Residues in contact with LEU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ILE* 3.7 26.9 - - + -
369D ILE* 2.9 27.6 + - + +
370D PHE* 3.6 3.1 - - + +
372D SER* 1.3 75.8 - - - +
374D LYS* 1.3 63.3 + - - +
376D GLN* 3.0 17.0 + - - +
378D LYS* 2.8 64.2 + - + +
379D VAL 4.8 0.7 - - - -
380D ILE* 3.7 29.6 - - + +
470D VAL* 4.0 23.3 - - + -
474D GLU* 5.7 1.1 - - - +
577D TYR* 4.0 2.2 - - + +
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Residues in contact with LYS 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D SER* 2.9 36.4 + - - +
95D ASP* 3.1 22.7 + - - +
98D ASN* 4.9 6.5 - - - +
370D PHE* 2.8 44.9 + - + +
371D ASN* 3.2 13.2 + - - +
373D LEU* 1.3 78.0 - - - +
375D GLU* 1.3 62.2 + - - +
377D ASN* 2.8 24.0 + - - +
378D LYS 4.2 8.0 + - - +
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Residues in contact with GLU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASN* 5.6 7.3 - - - +
371D ASN 3.1 8.4 + - - +
372D SER* 3.5 13.9 - - - +
374D LYS* 1.3 84.2 - - - +
376D GLN* 1.3 60.8 + - + +
377D ASN* 3.3 5.7 + - - -
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Residues in contact with GLN 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D SER* 3.0 36.8 + - - +
373D LEU* 3.0 16.9 + - - +
374D LYS 3.0 0.8 - - - -
375D GLU* 1.3 77.8 - - + +
377D ASN* 1.3 72.9 + - - +
378D LYS* 3.0 32.4 + - + +
474D GLU* 4.8 4.0 + - - -
477D LYS* 5.9 0.8 - - - +
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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