Contacts of the helix formed by residues 446 - 464 (chain A) in PDB entry 3SN5
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 446 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.9 14.1 - - - +
444A CYS* 3.2 14.8 - - - -
445A PRO* 1.3 80.4 - - - +
447A ARG* 1.4 50.7 + - - +
448A LEU 3.4 2.2 - - - -
449A PHE* 3.2 8.2 + - - +
450A ALA* 2.8 35.1 + - - +
601A HEM 3.8 22.9 - - - -
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Residues in contact with ARG 447 (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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134A GLN* 3.5 33.8 + - - +
437A PHE* 3.6 39.9 - - + -
443A ILE* 3.7 43.8 - - - +
444A CYS* 2.8 36.5 + - - +
445A PRO* 3.3 1.4 - - - +
446A GLY* 1.4 72.6 - - - +
448A LEU* 1.3 86.4 + - + +
450A ALA* 3.5 0.9 - - - +
451A ILE* 3.0 30.6 + - + +
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU 4.9 2.2 - - - +
134A GLN* 4.0 26.2 - - + -
135A GLY 5.6 1.1 - - - +
138A LEU* 3.6 27.6 - - + -
445A PRO 4.8 1.0 + - - -
446A GLY 3.4 0.8 - - - -
447A ARG* 1.3 98.8 - - + +
449A PHE* 1.4 56.3 + - - +
451A ILE* 3.4 4.1 + - - +
452A HIS* 3.0 39.0 + - + +
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Residues in contact with PHE 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 4.9 4.8 + - + +
138A LEU* 3.8 21.7 - - + +
141A LEU* 3.7 47.6 - - + -
142A THR* 4.4 4.7 - - - -
145A MET* 3.9 20.0 - - + -
183A GLY* 5.8 2.0 - - - -
186A THR* 4.0 19.1 - - + -
187A ILE* 4.4 16.6 - - + -
286A SER* 5.8 1.3 - - - -
446A GLY* 3.2 11.1 + - - +
448A LEU* 1.4 75.7 - - - +
450A ALA* 1.4 54.7 + - - +
452A HIS* 3.0 6.8 + - + +
453A GLU* 2.8 64.5 + - + +
456A GLN* 5.5 0.2 - - - -
601A HEM 3.9 20.0 - - + -
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 3.7 9.0 - - + -
446A GLY 2.8 21.2 + - - +
447A ARG 3.5 5.8 - - - +
449A PHE* 1.4 70.5 - - - +
451A ILE* 1.4 61.9 + - - +
453A GLU* 3.1 18.9 + - - +
454A ILE* 3.1 30.1 + - - +
601A HEM 3.6 41.5 - - + -
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Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ASP* 3.6 13.5 - - - +
350A ILE* 3.6 32.5 - - + -
351A LYS* 6.3 1.1 - - + -
354A LEU* 4.6 1.8 - - + -
434A TYR* 4.9 3.4 - - - +
437A PHE* 3.5 31.4 - - + -
447A ARG 3.0 20.6 + - - +
448A LEU* 4.0 4.5 - - - +
450A ALA* 1.4 72.0 - - - +
452A HIS* 1.3 67.2 + - + +
454A ILE* 3.5 6.5 + - + +
455A LYS* 3.0 52.3 + - - +
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Residues in contact with HIS 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.0 13.2 - - + +
142A THR* 3.0 34.5 + - + +
337A GLN* 3.0 43.1 + - + +
340A LEU* 4.3 14.0 - - + +
341A ASN* 2.9 29.9 + - - -
448A LEU* 3.0 19.1 + - + +
449A PHE* 3.0 11.8 + - + +
451A ILE* 1.3 78.0 - - + +
453A GLU* 1.4 57.8 + - - +
455A LYS* 3.3 13.3 + - - +
456A GLN* 2.9 35.1 + - - +
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 3.4 39.4 - - + +
149A LEU* 4.2 2.1 - - - +
179A MET* 4.0 9.6 - - + +
183A GLY* 5.0 4.2 - - - -
286A SER 4.4 2.7 - - - +
290A THR* 3.3 23.9 + - + +
449A PHE* 2.8 36.0 + - + +
450A ALA* 3.1 18.7 - - - +
452A HIS* 1.4 69.5 - - - +
454A ILE* 1.4 63.3 - - - +
456A GLN* 3.4 11.6 + - - +
457A PHE* 3.0 23.0 + - - +
601A HEM 3.1 30.4 - - - +
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Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 4.7 3.4 - - + +
293A ALA* 3.8 28.3 - - + -
294A THR* 3.6 24.9 - - + +
297A SER* 3.9 14.4 - - - +
350A ILE* 3.7 40.4 - - + -
450A ALA 3.1 20.7 + - - +
451A ILE* 4.0 6.1 - - + +
452A HIS 3.4 0.2 - - - -
453A GLU* 1.4 77.6 - - + +
455A LYS* 1.4 62.5 + - - +
457A PHE* 3.1 8.8 + - - +
458A LEU* 3.0 30.8 + - + +
601A HEM 4.3 12.3 - - + -
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Residues in contact with LYS 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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340A LEU* 3.2 43.4 + - + +
341A ASN* 4.1 9.9 + - - +
343A LEU* 3.9 14.8 - - + -
346A LEU* 4.2 13.9 - - + +
347A ASP* 2.9 46.6 + - - +
350A ILE* 3.7 13.7 - - + -
451A ILE* 3.0 29.0 + - - +
452A HIS* 3.4 12.1 - - - +
454A ILE* 1.4 75.1 - - - +
456A GLN* 1.3 50.6 + - - +
458A LEU* 3.2 6.1 + - - +
459A ILE* 2.8 42.7 + - + +
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Residues in contact with GLN 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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142A THR* 3.0 40.1 + - - +
145A MET* 3.4 29.5 - - - +
146A MET* 3.4 37.5 - - + +
149A LEU* 3.8 13.0 - - + -
335A LEU 5.4 2.0 + - - -
340A LEU* 3.9 15.6 - - + +
449A PHE* 5.5 0.3 - - - -
452A HIS* 2.9 21.3 + - - +
453A GLU* 3.7 10.8 - - - +
454A ILE 3.3 0.2 - - - -
455A LYS* 1.3 71.3 - - - +
457A PHE* 1.3 61.8 + - - +
459A ILE* 3.4 7.3 + - - +
460A LEU* 3.0 29.5 + - - +
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Residues in contact with PHE 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 4.0 8.2 - - + +
153A MET* 4.2 5.8 - - + -
174A PHE* 3.9 19.1 - + - -
175A CYS* 3.8 18.8 - - - -
178A VAL* 3.7 30.1 - - + -
179A MET* 3.7 25.4 - - + -
294A THR* 3.4 24.7 - - + -
298A LEU* 3.8 22.0 - - + -
453A GLU 3.0 14.6 + - - +
454A ILE 3.1 8.0 + - - +
456A GLN* 1.3 74.9 - - - +
458A LEU* 1.4 62.0 + - + +
460A LEU* 3.4 4.4 + - - +
461A MET* 2.9 61.0 + - + +
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Residues in contact with LEU 458 (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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294A THR 5.1 0.4 - - - +
297A SER* 4.2 8.3 - - - -
298A LEU* 4.0 33.2 - - + +
301A MET* 4.1 17.5 - - + -
315A VAL* 5.3 0.2 - - - -
346A LEU* 4.1 28.5 - - + -
349A ILE* 4.9 6.7 - - + -
350A ILE* 4.1 17.5 - - + -
454A ILE* 3.0 34.1 + - + +
455A LYS* 3.6 6.7 - - - +
457A PHE* 1.4 82.4 - - + +
459A ILE* 1.4 64.2 + - - +
461A MET* 3.7 4.8 - - - +
462A LEU* 3.0 32.9 + - - +
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Residues in contact with ILE 459 (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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146A MET* 4.9 1.1 - - + -
315A VAL* 3.8 37.0 - - + +
318A THR* 6.1 0.9 - - + -
319A LEU* 4.4 4.7 - - + -
333A ILE* 4.2 24.7 - - + -
335A LEU* 4.0 15.5 - - + -
340A LEU* 3.8 19.1 - - + -
343A LEU* 3.7 28.0 - - + -
346A LEU* 3.9 5.4 - - + -
455A LYS 2.8 25.4 + - - +
456A GLN* 3.8 6.1 - - - +
458A LEU* 1.4 71.7 - - - +
460A LEU* 1.4 56.7 + - + +
462A LEU* 3.4 2.3 + - - +
463A SER* 2.8 38.8 + - - +
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Residues in contact with LEU 460 (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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146A MET* 3.9 12.1 - - + -
149A LEU* 3.6 31.4 - - + -
150A GLN* 3.7 34.5 - - + +
153A MET* 3.7 22.2 - - + -
333A ILE* 3.9 27.1 - - + -
456A GLN 3.0 20.5 + - - +
459A ILE* 1.4 71.3 - - + +
461A MET* 1.3 60.2 + - - +
463A SER* 4.4 4.5 - - - -
464A TYR* 2.8 52.1 + - + +
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Residues in contact with MET 461 (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 MET* 3.7 14.8 - - + -
174A PHE* 3.6 33.9 - - + -
298A LEU* 3.9 27.6 - - + -
301A MET* 5.6 0.7 - - + -
457A PHE* 2.9 43.2 + - + +
458A LEU* 3.3 6.9 + - - +
460A LEU* 1.3 73.3 - - - +
462A LEU* 1.4 60.6 + - + +
465A PHE* 3.2 41.8 + - + +
467A LEU* 3.7 39.6 - - + +
497A PHE* 4.0 6.3 - - + -
499A TYR* 5.5 0.7 - - + -
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Residues in contact with LEU 462 (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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301A MET* 3.8 30.5 - - + -
308A MET* 3.7 28.5 - - + +
311A ALA* 4.0 13.9 - - + +
312A THR* 3.5 29.4 - - + +
315A VAL* 3.7 31.2 - - + -
346A LEU* 4.7 2.9 - - + -
458A LEU 3.0 22.2 + - - +
459A ILE 3.8 2.7 - - - +
461A MET* 1.4 74.7 - - - +
463A SER* 1.3 58.6 + - - +
465A PHE 3.6 6.1 - - - +
467A LEU* 4.8 2.9 - - + -
502A LYS* 3.0 25.8 + - - -
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Residues in contact with SER 463 (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 VAL* 3.7 5.2 - - - +
319A LEU* 3.4 25.3 - - - +
326A VAL* 4.2 26.0 - - - +
333A ILE* 6.3 0.9 - - - -
459A ILE* 2.8 22.8 + - - +
460A LEU* 3.8 7.6 - - - -
462A LEU* 1.3 76.2 - - - +
464A TYR* 1.3 67.6 + - - +
502A LYS* 3.9 15.1 - - - +
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Residues in contact with TYR 464 (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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150A GLN* 3.2 31.4 + - + +
153A MET* 4.0 34.3 - - + -
154A ARG* 3.4 38.9 + - + +
326A VAL* 4.9 14.1 - - + -
327A SER 5.3 5.8 - - - -
328A LEU* 5.4 7.9 - - + -
333A ILE* 6.2 2.5 - - + -
460A LEU* 2.8 41.9 + - + +
463A SER* 1.3 83.5 - - - +
465A PHE* 1.3 75.4 - + + +
501A PHE* 3.4 11.4 - + + +
502A LYS* 2.8 30.3 + - - +
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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