Contacts of the helix formed by residues 439 - 456 (chain A) in PDB entry 4GL5
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 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A LEU* 4.1 3.4 - - - -
437A CYS* 3.3 8.5 - - - -
438A ALA* 1.3 76.8 - - - +
440A LYS* 1.3 58.4 + - - +
441A TYR 2.9 4.2 + - - -
442A ILE* 3.2 13.4 + - - -
443A ALA* 2.8 34.3 + - - +
600A HEM 3.7 29.1 - - - +
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Residues in contact with LYS 440 (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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428A GLN* 4.4 7.9 + - - +
430A PHE* 3.5 59.4 - - + +
431A GLY 3.0 27.2 + - - +
432A PHE* 4.0 15.0 - - - +
436A GLY* 5.3 0.7 - - - -
437A CYS* 3.3 22.8 - - + +
438A ALA 3.2 4.0 - - - -
439A GLY* 1.3 77.2 - - - +
441A TYR* 1.3 105.8 + - + +
443A ALA* 4.6 0.2 - - - -
444A MET* 3.8 8.8 + - - +
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Residues in contact with TYR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET* 6.5 1.1 - - + -
152A LEU 4.9 6.1 - - - +
153A SER* 5.9 6.3 - - - -
157A LEU* 3.7 16.8 - - + -
438A ALA 4.7 4.0 + - - -
439A GLY 2.9 1.6 + - - -
440A LYS* 1.3 114.4 + - + +
442A ILE* 1.3 67.1 + - - +
443A ALA 3.0 2.4 + - - -
444A MET* 3.2 17.6 + - + +
445A VAL* 3.4 12.3 + - - +
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.8 51.8 + - + +
156A GLY 4.2 9.4 - - - +
157A LEU* 3.5 21.3 - - + +
160A MET* 3.8 46.4 - - + -
202A LEU* 4.3 2.2 - - + -
203A PHE* 4.3 5.4 - - + -
439A GLY* 3.2 16.6 + - - +
441A TYR* 1.3 77.0 - - - +
443A ALA* 1.3 62.2 + - - +
445A VAL* 3.0 5.9 + - + +
446A MET* 2.9 35.9 + - + +
600A HEM 4.5 10.1 - - + -
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Residues in contact with ALA 443 (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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311A MET* 3.9 13.7 - - - +
430A PHE* 4.1 16.2 - - + -
439A GLY 2.8 20.9 + - - +
440A LYS 4.3 0.2 - - - +
442A ILE* 1.3 74.6 - - - +
444A MET* 1.3 63.6 + - - +
446A MET* 2.9 8.9 + - - +
447A MET* 2.9 30.2 + - - +
600A HEM 3.9 30.1 - - + -
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Residues in contact with MET 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ILE* 6.0 1.3 - - + -
357A GLU* 4.0 19.7 - - + +
360A ILE* 4.2 18.8 - - + +
361A TYR* 3.8 42.0 - - + +
364A MET* 4.9 0.9 - - - -
430A PHE* 3.7 24.7 - - + -
440A LYS 3.8 5.7 + - - +
441A TYR* 3.2 11.8 + - + +
443A ALA* 1.3 76.9 - - - +
445A VAL* 1.3 61.3 + - + +
447A MET* 3.8 17.7 - - - +
448A LYS* 3.4 41.9 + - - +
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.8 36.8 - - + +
160A MET* 4.9 3.6 - - + -
161A VAL* 3.8 43.0 - - + +
347A ILE* 5.4 1.3 - - + -
350A ILE* 4.5 22.4 - - + -
441A TYR 3.4 7.6 + - - +
442A ILE* 3.0 10.2 + - + +
443A ALA 3.0 0.6 - - - -
444A MET* 1.3 77.6 - - + +
446A MET* 1.3 68.4 + - - +
448A LYS* 3.0 10.8 + - - +
449A ALA* 2.8 21.0 + - + +
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Residues in contact with MET 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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160A MET* 3.6 45.5 - - + +
164A CYS* 3.7 19.3 - - - -
195A MET* 3.6 21.8 - - + -
198A THR* 4.2 3.4 - - - -
199A SER* 5.8 0.2 - - - +
307A ALA* 4.1 6.7 - - + -
311A MET* 3.5 30.5 - - + -
442A ILE* 2.9 22.7 - - - +
443A ALA* 2.9 1.5 + - - +
445A VAL* 1.3 75.5 - - - +
447A MET* 1.3 58.2 + - - +
449A ALA* 3.8 1.7 - - - +
450A ILE* 2.9 35.7 + - - +
600A HEM 3.7 19.7 - - + -
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Residues in contact with MET 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A MET* 3.3 17.9 - - + +
314A SER* 4.6 7.0 - - - -
315A LEU* 3.6 24.5 - - + -
318A MET* 4.3 10.8 - - + +
360A ILE* 3.8 39.3 - - + -
364A MET* 4.3 5.6 - - - +
430A PHE* 4.3 0.9 - - + -
443A ALA* 2.9 28.2 + - + +
444A MET* 3.8 13.5 - - - +
446A MET* 1.3 73.8 - - - +
448A LYS* 1.3 67.5 + - - +
449A ALA 3.1 0.3 + - - -
450A ILE* 3.9 0.4 - - - +
451A LEU* 2.8 29.0 + - - +
600A HEM 3.5 33.2 - - + -
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Residues in contact with LYS 448 (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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345A ILE* 5.9 0.4 - - - -
350A ILE* 3.1 57.1 + - + +
351A GLN* 4.8 0.8 - - - +
353A LEU* 4.3 8.1 - - + -
356A MET* 3.3 31.9 - - + +
357A GLU* 3.0 51.8 + - - +
360A ILE* 3.7 14.1 - - + +
444A MET* 3.4 24.1 + - - +
445A VAL* 3.0 9.9 + - - +
447A MET* 1.3 76.0 - - - +
449A ALA* 1.3 58.7 + - - +
452A VAL* 2.9 27.4 + - - +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 3.9 35.0 - - + +
164A CYS* 4.1 12.3 - - + -
165A ALA* 5.1 1.6 - - - +
345A ILE* 5.0 12.1 - - + +
350A ILE* 5.9 0.6 - - - +
445A VAL 2.8 18.4 + - - +
446A MET* 3.8 4.9 - - - +
448A LYS* 1.3 73.8 - - - +
450A ILE* 1.3 53.4 + - - +
452A VAL* 3.3 6.3 + - - +
453A THR* 2.6 38.0 + - - +
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Residues in contact with ILE 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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164A CYS* 3.8 36.6 - - + +
168A LEU* 3.5 19.4 - - + +
191A LEU* 4.3 16.4 - - + -
194A VAL* 5.4 5.8 - - + -
195A MET* 5.2 11.4 - - + -
198A THR* 5.9 0.2 - - - +
315A LEU* 3.3 47.1 - - + -
319A LEU* 6.4 0.7 - - + -
446A MET 2.9 26.7 + - - +
449A ALA* 1.3 69.5 - - - +
451A LEU* 1.3 70.0 + - + +
453A THR* 3.7 4.9 - - - -
454A LEU* 3.1 30.7 + - + +
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Residues in contact with LEU 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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315A LEU* 3.9 15.5 - - + -
318A MET* 3.7 28.7 - - + -
319A LEU* 4.2 26.5 - - + -
322A ILE* 4.0 12.3 - - + -
332A ILE* 5.6 0.4 - - + -
356A MET* 3.8 23.3 - - + -
359A PHE* 3.7 25.6 - - + -
360A ILE* 4.8 1.1 - - + -
447A MET 2.8 19.7 + - - +
450A ILE* 1.3 78.0 - - + +
452A VAL* 1.3 69.7 + - - +
454A LEU* 4.6 3.6 - - + -
455A LEU* 3.0 32.3 + - + +
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Residues in contact with VAL 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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336A ILE* 3.9 28.7 - - + -
340A ILE* 4.3 10.8 - - + -
345A ILE* 4.3 19.3 - - + -
353A LEU* 4.0 15.0 - - + -
356A MET* 3.5 26.5 - - + -
448A LYS 2.9 14.3 + - - +
449A ALA* 3.3 6.5 + - - +
451A LEU* 1.3 76.3 - - - +
453A THR* 1.3 71.0 + - + +
456A ARG* 2.8 44.1 + - + +
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Residues in contact with THR 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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165A ALA* 4.4 27.1 - - + +
168A LEU* 3.4 22.8 - - - +
169A LYS* 4.7 20.9 - - + -
172A LEU* 4.4 6.9 - - - +
344A ASP* 5.6 0.7 - - - +
345A ILE* 4.6 7.4 - - + -
449A ALA 2.6 28.0 + - - +
450A ILE* 3.7 0.3 - - - -
451A LEU 3.5 0.2 - - - -
452A VAL* 1.3 81.9 - - + +
454A LEU* 1.3 60.6 + - - +
456A ARG* 3.7 27.8 - - + +
457A ARG* 3.9 8.5 - - - +
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Residues in contact with LEU 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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168A LEU* 4.0 9.6 - - + +
172A LEU* 4.6 12.1 - - + -
190A LEU* 5.8 2.7 - - + -
191A LEU* 5.4 9.0 - - + -
319A LEU* 3.8 38.4 - - + -
450A ILE* 3.1 23.0 + - + +
451A LEU* 3.9 6.1 - - + +
452A VAL 2.9 1.6 + - - -
453A THR* 1.3 75.0 - - - +
455A LEU* 1.3 59.6 + - + +
456A ARG 3.1 1.1 - - - -
457A ARG* 2.8 27.0 + - - +
458A PHE* 3.1 35.7 + - + -
460A VAL* 4.6 7.4 - - + -
492A PHE* 4.0 25.8 - - + -
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Residues in contact with LEU 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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319A LEU* 4.5 15.0 - - + -
322A ILE* 3.4 48.9 - - + -
329A GLU* 5.7 4.3 - - + +
332A ILE* 4.1 26.0 - - + -
333A ILE* 3.5 18.5 - - + +
336A ILE* 4.7 4.0 - - + -
451A LEU* 3.0 27.8 + - + +
452A VAL 4.1 0.4 - - - +
454A LEU* 1.3 80.7 - - + +
456A ARG* 1.3 58.1 + - - +
457A ARG 3.0 3.5 + - - -
458A PHE 3.9 11.7 - - - +
460A VAL* 4.7 8.5 - - + -
495A ARG* 2.8 31.6 + - - +
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Residues in contact with ARG 456 (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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169A LYS* 6.1 3.2 - - - +
333A ILE* 4.6 4.7 - - - +
336A ILE* 4.6 18.1 - - + +
340A ILE* 3.3 27.3 - - - +
341A GLY 3.5 16.3 + - - -
342A GLU* 4.2 13.4 + - - +
343A ARG 2.8 29.6 + - - -
344A ASP* 4.8 4.2 - - - +
345A ILE* 4.9 1.6 - - - +
452A VAL* 2.8 29.7 + - + +
453A THR* 3.7 25.9 - - + +
454A LEU 3.0 0.2 + - - -
455A LEU* 1.3 76.0 - - - +
457A ARG* 1.3 60.9 + - + +
495A ARG* 4.3 9.3 - - - +
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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