Contacts of the helix formed by residues 441 - 459 (chain C) in PDB entry 4EJJ
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 441 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 5.6 0.7 - - - -
439C CYS* 3.1 15.3 - - - -
440C PHE* 1.3 79.4 - - - +
442C GLU* 1.3 67.2 + - - +
443C GLY 3.2 3.0 + - - -
444C LEU* 3.3 8.9 + - - +
445C ALA* 3.1 19.8 + - - +
500C HEM 3.8 33.4 - - - -
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Residues in contact with GLU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C PHE* 5.7 0.7 - - - -
432C PHE* 3.4 49.2 - - + +
433C SER 5.1 2.1 - - - +
438C ASN* 4.3 15.2 + - - -
439C CYS* 3.1 17.0 + - - +
440C PHE 3.3 1.8 - - - -
441C GLY* 1.3 76.3 - - - +
443C GLY* 1.3 56.2 + - - +
445C ALA* 3.0 1.4 + - - +
446C ARG* 2.9 70.6 + - - +
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Residues in contact with GLY 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 4.9 5.8 - - - -
141C GLY* 5.8 5.4 - - - -
343C PHE* 5.6 1.7 - - - -
440C PHE 4.9 2.0 + - - -
441C GLY 3.3 0.4 - - - -
442C GLU* 1.3 80.3 - - - +
444C LEU* 1.4 55.0 + - - +
446C ARG* 3.6 7.0 + - - +
447C MET* 3.1 27.4 + - - +
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Residues in contact with LEU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 6.2 1.6 - - + -
140C VAL* 3.9 26.7 - - + +
145C ILE* 4.1 17.3 - - + -
149C ILE* 3.8 14.1 - - + -
181C VAL* 3.6 28.9 - - + -
182C ILE* 4.4 15.5 - - + -
185C ILE* 4.9 6.1 - - + -
302C GLY* 5.5 0.4 - - - -
441C GLY* 3.3 10.6 + - - +
443C GLY* 1.4 71.6 - - - +
445C ALA* 1.3 60.8 + - - +
447C MET* 3.8 5.5 - - - -
448C GLU* 3.0 39.6 + - - +
500C HEM 4.2 32.1 - - + -
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C VAL* 3.8 15.9 - - + +
432C PHE* 3.7 22.7 - - + -
441C GLY 3.1 11.7 + - - +
442C GLU 3.0 8.4 + - - +
444C LEU* 1.3 75.3 - - - +
446C ARG* 1.3 61.5 + - - +
448C GLU* 3.0 2.9 + - - +
449C LEU* 2.9 36.7 + - + +
500C HEM 3.7 22.6 - - + +
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Residues in contact with ARG 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C PHE* 4.1 12.0 - - + -
346C ARG* 4.7 17.1 - - - +
353C GLU* 4.8 2.4 + - - -
356C ILE* 5.9 0.6 - - - +
357C HIS* 3.0 37.5 + - - -
360C GLN* 5.2 4.6 - - - +
423C PHE* 5.6 1.4 - - - -
429C PHE* 4.7 12.2 - - - -
432C PHE* 4.0 16.8 - - + -
442C GLU* 2.9 53.1 + - - +
443C GLY* 3.8 7.0 - - - +
445C ALA* 1.3 76.0 - - - +
447C MET* 1.3 61.8 + - - +
449C LEU* 4.0 7.6 - - - +
450C PHE* 3.2 24.3 + - - +
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Residues in contact with MET 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLY* 4.8 9.2 - - - +
142C LYS 4.2 23.3 - - - +
145C ILE* 3.8 18.8 - - + -
146C GLU* 3.8 33.7 - - + +
149C ILE* 3.9 10.3 - - + -
343C PHE* 3.8 43.9 - - + -
443C GLY 3.1 17.0 + - - +
444C LEU* 4.0 7.0 - - - +
445C ALA 3.1 0.8 - - - -
446C ARG* 1.3 78.8 - - - +
448C GLU* 1.3 61.4 + - - +
450C PHE* 4.1 0.9 - - - +
451C LEU* 3.1 31.4 + - + +
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Residues in contact with GLU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ILE* 3.6 23.3 - - + -
178C VAL* 3.7 11.1 - - - +
181C VAL* 3.0 33.2 - - - +
182C ILE 4.6 0.5 + - - -
302C GLY 4.3 3.5 - - - +
306C VAL* 3.5 29.9 - - + +
444C LEU* 3.0 28.9 + - - +
445C ALA* 3.0 5.1 + - - +
447C MET* 1.3 76.5 - - - +
449C LEU* 1.3 56.6 + - - +
452C PHE* 2.8 64.2 + - + +
500C HEM 5.3 0.9 - - - +
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C VAL* 3.9 20.6 - - + -
309C THR* 3.8 24.2 - - + -
310C LEU* 3.6 24.9 - - + -
356C ILE* 3.9 20.6 - - + -
360C GLN* 3.3 40.2 - - + +
432C PHE* 5.2 1.1 - - + -
445C ALA 2.9 22.6 + - - +
446C ARG* 4.0 5.6 - - - +
448C GLU* 1.3 75.1 - - - +
450C PHE* 1.3 66.7 + - - +
453C PHE* 2.9 32.8 + - + +
500C HEM 5.0 5.4 - - + -
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Residues in contact with PHE 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C PRO* 4.9 1.6 - - + -
342C LYS 3.6 21.3 - - - -
343C PHE* 4.6 13.0 - + + -
345C ASP* 3.9 6.5 - - + -
346C ARG* 3.7 45.8 - - + -
349C MET* 4.0 17.7 - - + -
352C MET* 3.9 17.7 - - + -
353C GLU* 5.1 5.4 - - - -
356C ILE* 3.4 22.7 - - + +
446C ARG 3.2 14.5 + - - +
447C MET 4.1 2.0 - - - +
449C LEU* 1.3 79.1 - - - +
451C LEU* 1.3 71.9 + - + +
454C THR* 2.7 59.8 + - + -
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLU* 4.2 19.5 - - + +
149C ILE* 3.8 33.2 - - + -
150C GLN* 4.3 12.8 - - + +
153C ALA* 5.2 1.8 - - + -
341C PRO* 3.7 26.7 - - + +
342C LYS 3.9 14.1 - - - -
343C PHE* 4.0 3.8 - - + +
447C MET* 3.1 35.5 + - + +
450C PHE* 1.3 94.6 - - + +
452C PHE* 1.3 56.2 + - - +
454C THR* 4.8 0.2 - - - -
455C THR* 2.7 44.1 + - - +
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Residues in contact with PHE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ILE* 3.8 17.3 - - + -
152C GLU* 4.5 1.6 - - + -
153C ALA* 3.6 31.2 - - + -
156C LEU* 4.9 7.2 - - + -
177C THR* 3.1 44.9 - - + -
178C VAL* 4.3 11.0 - - + -
181C VAL* 4.0 7.6 - - + -
306C VAL* 4.9 0.2 - - + -
310C LEU* 4.0 30.1 - - + -
314C PHE* 5.4 1.6 - - + -
448C GLU* 2.8 58.9 + - + +
451C LEU* 1.3 70.7 - - - +
453C PHE* 1.3 62.4 + - - +
455C THR* 4.2 2.8 - - - -
456C VAL* 3.0 30.9 + - + +
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Residues in contact with PHE 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C THR* 3.8 4.5 - - + -
310C LEU* 3.5 41.1 - - + -
313C GLY* 3.7 21.3 - - - -
314C PHE* 3.5 36.8 - + - -
317C LEU* 4.7 5.2 - - + -
352C MET* 4.1 10.1 - - + -
356C ILE* 4.0 31.0 - - + -
359C ILE* 3.7 21.3 - - + -
449C LEU* 2.9 32.0 + - + +
450C PHE 4.2 0.9 - - - +
452C PHE* 1.3 75.9 - - - +
454C THR* 1.3 64.2 + - - +
456C VAL* 3.2 2.6 + - - +
457C MET* 2.9 30.7 + - + +
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Residues in contact with THR 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ILE* 3.8 12.9 - - + +
335C ILE* 4.1 15.5 - - + -
341C PRO* 3.8 23.6 - - + -
349C MET* 4.5 4.9 - - + -
352C MET* 3.1 36.1 - - + +
450C PHE* 2.7 39.2 + - + -
451C LEU 4.1 0.7 - - - -
453C PHE* 1.3 75.2 - - - +
455C THR* 1.3 65.0 + - - +
458C GLN* 2.9 23.0 + - - +
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Residues in contact with THR 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLN* 6.1 0.2 - - - -
153C ALA* 3.9 28.0 - - + +
154C GLY* 4.8 1.6 - - - +
157C ILE* 3.6 19.0 - - + +
340C GLN* 5.5 7.0 - - + -
341C PRO* 3.4 34.4 + - + +
451C LEU* 2.7 23.4 + - - +
452C PHE 4.2 1.6 - - - -
454C THR* 1.3 80.7 - - - +
456C VAL* 1.3 57.9 + - - +
458C GLN* 3.5 7.5 - - - +
459C ASN* 3.2 26.2 + - - +
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Residues in contact with VAL 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 3.6 30.3 - - + -
157C ILE* 3.9 10.3 - - + -
160C LEU* 4.1 10.3 - - + -
174C LEU* 5.7 0.2 - - + -
314C PHE* 3.8 25.4 - - + -
452C PHE 3.0 22.9 + - - +
453C PHE 3.8 2.5 - - - +
455C THR* 1.3 73.7 - - - +
457C MET* 1.3 69.1 + - + +
459C ASN 3.5 1.2 + - - -
460C PHE* 3.1 30.0 + - + +
491C PHE* 3.8 30.3 - - + -
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Residues in contact with MET 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C PHE* 4.6 5.6 - - + -
317C LEU* 3.6 32.5 - - + -
324C GLU* 4.3 9.2 - - - +
327C VAL* 4.2 9.0 - - + -
328C HIS* 2.9 35.9 + - + +
331C ILE* 3.6 19.1 - - + -
352C MET* 4.3 7.6 - - + -
453C PHE* 2.9 23.7 + - + +
456C VAL* 1.3 82.4 - - + +
458C GLN* 1.3 65.7 - - - +
460C PHE 3.0 21.0 - - - +
462C LEU* 3.5 35.2 - - + -
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Residues in contact with GLN 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ILE* 3.6 22.8 - - + +
335C ILE* 3.6 8.7 - - - +
336C GLY 3.2 27.8 + - - +
337C LYS* 4.3 19.8 - - + +
338C ASN 4.8 0.6 - - - -
339C ARG 2.8 26.7 + - - +
340C GLN* 4.8 0.3 - - - -
341C PRO* 3.6 21.1 - - + +
454C THR 2.9 19.0 + - - +
455C THR* 3.5 6.2 - - - +
456C VAL 3.3 0.2 - - - -
457C MET* 1.3 75.4 - - - +
459C ASN* 1.3 74.3 + - - +
494C ARG* 2.9 28.6 + - - +
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Residues in contact with ASN 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 3.8 18.9 - - + +
161C ARG* 2.5 33.5 + - - +
455C THR* 3.2 18.5 + - - +
456C VAL 3.5 1.0 + - - -
457C MET 3.3 0.4 - - - -
458C GLN* 1.3 108.9 + - - +
460C PHE* 1.3 88.0 + - + +
493C PRO* 4.0 1.9 - - - +
494C ARG* 3.7 17.6 + - - -
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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