Contacts of the helix formed by residues 364 - 376 (chain D) in PDB entry 1FM9
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 MET 364 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D 570 3.5 55.2 - - + +
285D CYS* 4.7 3.1 - - - -
330D LEU* 4.0 15.0 - - + -
334D MET* 3.6 30.1 - - + -
339D VAL* 4.9 1.3 - - + -
353D LEU* 3.8 33.0 - - + -
356D LEU* 6.3 0.2 - - + -
360D PHE 5.1 0.6 + - - +
361D GLY 5.4 1.0 + - - -
362D ASP* 4.6 0.2 - - - +
363D PHE* 1.3 80.7 - - + +
365D GLU* 1.3 56.5 + - - +
366D PRO* 3.2 3.4 - - - -
367D LYS* 2.7 31.3 + - + +
368D PHE* 3.0 29.5 + - + -
449D HIS* 6.5 0.4 - - - -
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Residues in contact with GLU 365 (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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350D ARG* 3.3 48.1 + - - +
354D LYS* 4.0 37.8 + - + +
361D GLY 5.2 1.3 + - - +
362D ASP* 4.4 14.9 + - + +
364D MET* 1.3 77.9 - - - +
366D PRO* 1.3 67.6 - - + +
368D PHE* 3.3 3.7 + - - +
369D GLU* 3.0 41.4 + - - +
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Residues in contact with PRO 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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362D ASP* 3.3 18.4 - - + +
363D PHE 3.3 13.2 - - - +
364D MET 3.2 4.9 - - - -
365D GLU* 1.3 95.1 - - + +
367D LYS* 1.3 63.6 + - + +
369D GLU* 3.4 15.2 + - + +
370D PHE* 3.0 27.7 + - - +
445D ILE* 4.8 11.4 - - + +
448D GLU* 3.4 34.8 - - + +
452D LEU* 5.3 1.6 - - + -
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Residues in contact with LYS 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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200D 570 5.4 1.3 - - + -
327D TYR* 4.1 21.5 - - + -
330D LEU* 4.0 29.2 - - + -
334D MET* 3.8 7.3 - - + +
363D PHE* 2.8 34.4 + - - +
364D MET* 2.7 22.2 + - + +
366D PRO* 1.3 81.2 - - - +
368D PHE* 1.3 57.8 + - - -
370D PHE* 3.5 9.5 + - + +
371D ALA* 2.8 28.9 + - - +
445D ILE* 4.0 24.4 + - + -
448D GLU* 5.5 1.2 - - - +
449D HIS* 2.8 45.4 + - - +
452D LEU* 5.1 2.4 - - - +
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Residues in contact with PHE 368 (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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334D MET* 3.7 21.5 - - + -
335D ASN 3.7 15.3 - - - -
338D GLY* 3.2 33.9 - - - -
339D VAL* 3.7 23.3 - - + -
350D ARG* 3.6 58.8 - - + +
353D LEU* 4.0 5.2 - - + -
364D MET* 3.0 41.4 + - + -
365D GLU* 3.3 7.4 + - - +
367D LYS* 1.3 73.2 - - - +
369D GLU* 1.3 57.3 + - - +
371D ALA* 3.0 3.7 + - + +
372D VAL* 2.7 40.3 + - + +
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Residues in contact with GLU 369 (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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350D ARG* 4.6 8.0 - - - +
365D GLU* 3.0 49.3 + - - +
366D PRO* 3.6 12.9 - - - +
368D PHE* 1.3 76.4 - - - +
370D PHE* 1.3 62.2 + - - +
372D VAL* 3.6 5.8 + - - +
373D LYS* 3.3 40.7 + - - +
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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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327D TYR* 3.5 28.3 - - + -
328D THR* 4.2 4.9 - - - -
331D ALA* 4.6 2.2 - - + -
366D PRO 3.0 13.5 + - - +
367D LYS* 3.6 8.5 - - + +
369D GLU* 1.3 74.5 - - - +
371D ALA* 1.3 57.7 + - - +
373D LYS* 3.1 9.2 + - + +
374D PHE* 2.7 61.0 + + + +
438D LYS* 4.1 24.5 - - + -
441D ASP* 4.3 13.5 - - + -
442D LEU* 3.4 36.1 - - + -
445D ILE* 3.2 31.9 - - + -
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Residues in contact with ALA 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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331D ALA* 3.8 26.0 - - + -
334D MET* 3.4 30.5 - - + -
335D ASN 6.0 0.4 - - - +
367D LYS 2.8 19.2 + - - +
368D PHE* 3.4 4.9 - - + +
370D PHE* 1.3 77.7 - - + +
372D VAL* 1.3 54.7 + - + +
374D PHE* 3.1 0.4 + - - -
375D ASN* 2.7 43.9 + - - +
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Residues in contact with VAL 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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335D ASN 5.1 3.4 - - - +
336D LYS* 3.9 53.4 - - + +
350D ARG* 4.1 15.9 - - - +
368D PHE* 2.7 24.2 + - + +
369D GLU* 3.8 7.2 - - - +
371D ALA* 1.3 73.4 - - + +
373D LYS* 1.3 67.5 + - + +
375D ASN* 4.0 5.5 - - - +
376D ALA* 3.2 20.8 + - + +
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Residues in contact with LYS 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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379A ASP* 2.9 35.9 - - - +
369D GLU* 3.3 26.9 + - - +
370D PHE* 3.1 10.6 + - + +
372D VAL* 1.3 84.8 - - + +
374D PHE* 1.3 62.7 + - - +
376D ALA* 3.4 17.9 + - - +
377D LEU* 4.1 5.7 + - - +
438D LYS* 3.6 29.8 + - - +
441D ASP* 5.5 1.1 - - - +
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Residues in contact with PHE 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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230D LYS* 5.8 2.0 - - - -
328D THR* 3.8 26.5 - - + -
331D ALA* 4.2 9.2 - - + -
332D SER* 6.0 0.7 - - - -
370D PHE* 2.7 48.8 + + + +
371D ALA* 3.7 5.2 - - - +
373D LYS* 1.3 74.6 - - - +
375D ASN* 1.3 74.6 + - - +
377D LEU* 3.1 24.6 + - + +
379D LEU* 3.9 13.1 - - + +
384D LEU* 3.7 28.0 - - + -
387D PHE* 3.9 14.1 - + - -
435D LEU* 3.7 25.8 - - + -
438D LYS* 3.7 23.0 - - + +
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Residues in contact with ASN 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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230D LYS* 4.1 20.7 + - - +
234D ARG* 3.6 14.4 + - - +
331D ALA* 3.0 39.7 + - - +
332D SER* 4.4 1.2 - - - +
334D MET 3.1 16.6 - - - +
335D ASN* 5.0 1.0 - - - -
371D ALA 2.7 26.6 + - - +
372D VAL* 4.0 5.2 - - - +
374D PHE* 1.3 73.3 - - - +
376D ALA* 1.3 56.3 + - - +
377D LEU 3.0 6.1 - - - -
378D GLU* 2.9 25.1 + - - +
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Residues in contact with ALA 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 VAL* 3.2 13.3 + - + +
373D LYS* 3.5 14.6 - - - +
374D PHE 3.1 1.0 - - - -
375D ASN* 1.3 76.4 - - - +
377D LEU* 1.3 61.1 + - + +
378D GLU* 3.1 12.0 + - - +
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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