Contacts of the helix formed by residues 437 - 455 (chain A) in PDB entry 5A5J
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 GLY 437 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 5.4 0.7 - - - -
435A CYS* 3.0 13.8 - - - -
436A VAL* 1.3 80.7 - - - +
438A GLU* 1.3 54.4 + - - +
439A ALA 3.2 2.9 - - - -
440A LEU* 4.0 7.2 - - - -
441A ALA* 2.7 38.0 + - - +
1493A HEM 3.6 25.3 - - - -
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A PHE* 3.8 42.3 - - + +
434A ILE* 4.1 27.9 - - + +
435A CYS* 3.2 16.4 + - - +
436A VAL 3.5 1.2 + - - -
437A GLY* 1.3 75.7 - - - +
439A ALA* 1.3 58.7 + - - +
441A ALA* 3.8 1.4 - - - +
442A GLY* 3.1 23.9 + - - -
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 6.1 0.7 - - - +
132A ARG* 5.0 19.7 - - + +
339A MET* 5.3 1.9 - - - +
342A ARG* 5.6 0.5 + - - -
437A GLY* 3.2 1.0 - - - -
438A GLU* 1.3 81.1 - - + +
440A LEU* 1.3 55.5 + - - +
442A GLY* 3.6 2.5 + - - -
443A MET* 2.9 38.8 + - + +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 5.8 10.1 - - + +
141A ILE* 3.2 35.2 - - + -
145A VAL* 4.0 15.3 - - + -
178A ILE* 4.2 3.8 - - + -
181A ILE* 4.1 25.8 - - + -
437A GLY* 3.5 9.9 + - - +
439A ALA* 1.3 75.3 - - - +
441A ALA* 1.3 69.1 + - - +
442A GLY 3.1 1.1 - - - -
443A MET* 3.1 9.4 + - + +
444A GLU* 2.9 44.5 + - - +
1493A HEM 3.7 33.4 - - + -
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Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 4.6 4.5 - - - +
428A PHE* 3.4 29.2 - - + -
437A GLY 2.7 23.6 + - - +
440A LEU* 1.3 75.1 - - - +
442A GLY* 1.3 56.9 + - - +
444A GLU* 3.1 3.6 + - - +
445A LEU* 2.9 34.1 + - - +
1493A HEM 3.4 34.2 - - + +
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Residues in contact with GLY 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 4.2 15.6 + - - -
352A VAL* 5.8 1.8 - - - +
356A GLN* 5.4 2.0 - - - -
428A PHE* 4.6 3.0 - - - -
438A GLU 3.1 11.3 + - - -
439A ALA* 3.6 5.8 - - - -
440A LEU 3.1 0.4 - - - -
441A ALA* 1.3 76.9 - - - +
443A MET* 1.3 62.0 + - - +
445A LEU* 4.1 8.9 - - - +
446A PHE* 3.2 25.8 + - - +
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Residues in contact with MET 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 4.0 23.6 - - + +
142A GLU* 3.6 44.4 - - + +
145A VAL* 4.1 12.6 - - + -
339A MET* 4.0 33.1 - - + +
439A ALA* 2.9 25.7 + - + +
440A LEU* 3.1 13.0 + - - +
442A GLY* 1.3 73.7 - - - +
444A GLU* 1.3 57.1 + - - +
447A LEU* 2.8 38.9 + - + +
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 3.7 28.9 - - + -
174A PRO* 3.1 39.4 - - - +
177A VAL* 3.6 16.4 - - - +
178A ILE* 5.0 0.9 - - - +
298A GLY 5.1 0.2 - - - +
302A THR* 3.5 16.4 - - + +
306A LEU* 4.8 0.9 - - - -
440A LEU* 2.9 49.2 + - - +
441A ALA 3.9 2.5 - - - +
443A MET* 1.3 68.5 - - - +
445A LEU* 1.3 67.6 + - - +
448A PHE* 2.9 45.5 + - + +
1493A HEM 4.3 2.6 - - - +
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Residues in contact with LEU 445 (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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302A THR* 4.3 7.0 - - + +
305A THR* 3.5 34.8 - - + +
306A LEU* 3.8 26.2 - - + +
352A VAL* 4.0 19.3 - - + -
356A GLN* 3.5 35.4 - - + +
441A ALA* 2.9 23.2 + - + +
442A GLY* 4.1 4.9 - - - +
444A GLU* 1.3 76.8 - - - +
446A PHE* 1.3 58.2 + - - +
449A LEU* 3.0 42.7 + - + +
1493A HEM 4.1 12.3 - - + -
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Residues in contact with PHE 446 (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 ILE* 5.2 1.1 - - + -
337A PRO* 5.1 0.9 - - + -
338A CYS 3.7 24.7 - - - -
339A MET* 4.2 13.0 - - + -
341A ASP* 4.3 2.2 - - + -
342A ARG* 3.7 46.9 - - + +
345A MET* 4.1 14.1 - - + -
348A THR* 3.4 35.0 - - + -
349A ASP* 5.2 1.8 - - - -
352A VAL* 4.8 15.5 - - + -
442A GLY 3.2 18.9 + - - +
443A MET 4.1 0.7 - - - +
444A GLU 3.1 0.4 - - - -
445A LEU* 1.3 74.5 - - + +
447A LEU* 1.3 75.5 - - + +
449A LEU* 4.3 1.1 - - - +
450A THR* 2.7 50.2 + - + +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 4.5 15.7 - - + +
145A VAL* 3.9 30.3 - - + -
146A GLN* 4.5 15.7 - - + +
149A ALA* 4.8 7.2 - - + -
337A PRO* 3.9 8.3 - - + +
338A CYS* 3.6 37.0 - - - +
339A MET* 4.0 13.9 - - - -
443A MET* 2.8 21.0 + - + +
446A PHE* 1.3 89.6 - - + +
448A PHE* 1.3 65.8 + - + +
450A THR* 3.0 15.4 + - - -
451A SER* 3.0 18.1 + - - +
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 3.3 37.9 - - + -
148A GLU* 4.2 2.7 - - + -
149A ALA* 3.7 24.7 - - + -
152A LEU* 3.8 19.1 - - + -
170A LEU* 6.1 0.2 - - + -
173A ALA* 3.6 25.8 - - + -
174A PRO 4.3 2.2 - - - -
177A VAL* 4.2 14.8 - - + -
306A LEU* 3.7 30.3 - - + -
444A GLU* 2.9 42.0 + - + +
447A LEU* 1.3 75.9 - - - +
449A LEU* 1.3 63.5 + - - +
451A SER* 3.2 5.8 + - - -
452A ILE* 2.9 30.6 + - + +
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Residues in contact with LEU 449 (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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306A LEU* 3.9 18.6 - - + +
309A ALA* 3.7 28.5 - - + -
310A LEU* 3.7 30.3 - - + -
313A LEU* 4.9 4.9 - - + -
351A VAL* 5.9 4.0 - - + -
352A VAL* 4.5 21.5 - - + -
355A VAL* 5.7 1.6 - - + -
445A LEU* 3.0 36.5 + - + +
446A PHE* 4.3 1.3 - - - +
447A LEU 3.3 0.2 - - - -
448A PHE* 1.3 79.0 - - - +
450A THR* 1.3 58.1 + - + +
452A ILE* 3.2 10.7 + - + +
453A LEU* 2.9 42.0 + - + +
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Residues in contact with THR 450 (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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323A VAL* 5.7 0.7 - - + -
327A ILE* 4.0 27.5 - - + +
331A ILE* 5.1 1.8 - - - -
337A PRO* 3.6 23.5 - - - +
345A MET* 4.5 2.2 - - + -
348A THR* 3.9 14.8 - - + -
446A PHE* 2.7 50.5 + - + +
447A LEU* 3.0 9.9 + - - -
449A LEU* 1.3 73.2 - - + +
451A SER* 1.3 55.3 + - - +
453A LEU* 3.0 2.2 + - + +
454A GLN* 2.7 37.7 + - - +
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Residues in contact with SER 451 (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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149A ALA* 3.8 20.5 - - - +
152A LEU* 6.1 0.9 - - - -
153A VAL* 4.0 19.5 - - - +
337A PRO* 4.0 16.7 - - - +
447A LEU* 3.0 19.1 + - - +
448A PHE* 3.4 7.0 - - - -
450A THR* 1.3 76.5 + - - +
452A ILE* 1.3 66.1 + - - +
454A GLN* 3.0 20.8 + - - -
455A ASN* 3.1 18.5 + - - +
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Residues in contact with ILE 452 (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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152A LEU* 4.8 8.3 - - + -
153A VAL* 4.7 3.6 - - + -
156A LEU* 4.1 16.2 - - + -
170A LEU* 4.4 22.7 - - + -
306A LEU* 5.5 0.2 - - + -
310A LEU* 4.5 14.1 - - + -
448A PHE* 2.9 31.5 + - + +
449A LEU* 3.5 20.9 - - + +
451A SER* 1.3 78.7 - - - +
453A LEU* 1.3 66.2 + - + +
454A GLN 3.2 0.5 + - - -
455A ASN 3.4 2.1 + - - -
456A PHE* 3.3 29.2 + - + +
458A LEU* 4.4 9.9 - - + -
487A PHE* 3.8 29.4 - - + -
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Residues in contact with LEU 453 (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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310A LEU* 5.7 0.4 - - + -
313A LEU* 3.9 28.3 - - + -
320A THR* 3.9 28.7 - - + +
323A VAL* 3.9 21.5 - - + -
324A GLN* 3.1 40.3 + - + +
327A ILE* 3.5 20.7 - - + +
449A LEU* 2.9 31.4 + - + +
450A THR* 3.0 2.2 + - + +
452A ILE* 1.3 82.6 - - + +
454A GLN* 1.3 59.5 + - - +
455A ASN 3.3 0.2 - - - -
456A PHE 3.8 3.1 - - - +
458A LEU* 4.3 15.9 - - + -
490A ILE* 3.8 2.8 - - - +
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Residues in contact with GLN 454 (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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327A ILE* 4.0 21.1 - - + -
331A ILE* 3.6 12.3 - - - +
332A GLY 2.8 30.0 + - - +
333A ARG* 4.2 18.1 - - - +
335A ARG 3.0 24.9 + - - +
336A SER* 5.2 0.2 - - - -
337A PRO* 3.7 21.2 - - + +
450A THR 2.7 13.2 + - - +
451A SER* 3.0 8.7 + - - +
453A LEU* 1.3 76.1 - - - +
455A ASN* 1.3 75.9 + - - +
456A PHE 3.6 0.2 - - - -
490A ILE* 3.4 20.6 - - - +
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Residues in contact with ASN 455 (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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153A VAL* 3.8 16.6 - - + +
157A ARG* 2.9 30.3 + - - +
451A SER* 3.1 10.9 + - - +
454A GLN* 1.3 107.0 + - - +
456A PHE* 1.3 86.5 + - + +
489A PRO* 3.4 3.8 - - - +
490A ILE* 3.3 25.5 + - - +
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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