Contacts of the helix formed by residues 452 - 470 (chain C) in PDB entry 4DVQ
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 452 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C VAL* 4.7 4.3 - - - -
450C CYS* 3.3 8.1 - - - -
451C LEU* 1.3 78.5 - - - +
453C ARG* 1.3 54.1 + - - +
454C ARG 3.2 2.5 - - - -
455C LEU* 3.0 8.3 + - - +
456C ALA* 2.7 36.3 + - - +
601C HEM 3.6 35.7 - - - +
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Residues in contact with ARG 453 (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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149C LEU* 4.3 5.6 - - + +
366C ARG* 4.7 1.4 - - - +
440C HIS* 5.7 1.6 - - - -
443C PHE* 3.4 58.1 - - + -
449C GLN* 3.7 23.6 + - - -
450C CYS* 3.4 14.5 - - - +
451C LEU 3.4 2.4 - - - -
452C GLY* 1.3 77.5 - - - +
454C ARG* 1.3 95.4 + - - +
456C ALA* 3.4 1.2 + - - +
457C GLU* 2.8 59.2 + - - +
603C SO4 2.7 27.5 + - - -
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Residues in contact with ARG 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL 5.4 0.2 + - - -
149C LEU* 2.6 59.3 + - + +
150C SER* 4.4 2.4 - - - +
151C PRO* 4.2 24.1 - - - +
154C VAL* 3.3 32.9 - - + +
157C PHE* 4.3 4.0 - - + -
452C GLY 3.2 0.4 - - - -
453C ARG* 1.3 102.5 - - - +
455C LEU* 1.3 61.0 + - - +
457C GLU* 3.9 5.8 - - - +
458C ALA* 3.0 28.4 + - - +
603C SO4 3.2 41.7 + - - +
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL* 4.9 5.2 + - + +
157C PHE* 3.6 30.9 - - + -
161C VAL* 4.0 8.7 - - + -
200C SER* 5.0 4.3 - - - +
203C ALA* 3.5 28.5 - - + -
204C LEU* 4.6 12.1 - - + -
289C ILE* 3.9 20.6 - - + -
315C SER* 5.3 1.8 - - - -
452C GLY* 3.0 11.9 + - - +
454C ARG* 1.3 74.4 - - - +
456C ALA* 1.3 66.8 + - - +
458C ALA* 3.2 1.9 + - - +
459C GLU* 3.0 48.2 + - - +
601C HEM 4.3 21.3 - - + -
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Residues in contact with ALA 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C THR* 4.1 13.9 - - + +
443C PHE* 4.5 2.2 - - + -
452C GLY 2.7 20.2 + - - +
453C ARG* 3.5 6.5 - - - +
455C LEU* 1.3 73.2 - - - +
457C GLU* 1.3 63.8 + - - +
459C GLU* 3.3 3.3 + - - +
460C MET* 3.2 30.3 + - - +
601C HEM 3.9 45.0 - - + +
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Residues in contact with GLU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ARG* 3.9 18.6 + - - +
369C LEU* 4.1 18.5 - - + +
370C LYS* 5.5 5.0 - - - +
373C LEU* 6.1 0.7 - - + -
440C HIS* 4.5 8.5 + - - -
443C PHE* 3.6 26.8 - - + -
453C ARG* 2.8 59.4 + - - +
454C ARG* 4.0 6.3 - - - +
456C ALA* 1.3 71.9 - - - +
458C ALA* 1.3 58.9 + - - +
460C MET* 3.2 5.0 + - - +
461C LEU* 2.8 34.3 + - + +
603C SO4 3.8 5.0 + - - -
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Residues in contact with ALA 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C VAL* 5.4 1.3 - - + -
157C PHE* 4.3 11.4 - - + -
158C LEU* 3.7 31.2 - - + -
161C VAL* 4.1 8.5 - - + -
359C THR* 6.3 1.1 - - + -
454C ARG 3.0 19.5 + - - +
455C LEU 3.2 5.4 + - - +
457C GLU* 1.3 77.2 - - - +
459C GLU* 1.3 61.8 + - - +
461C LEU* 4.4 5.8 - - - -
462C LEU* 3.1 29.6 + - - +
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Residues in contact with GLU 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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161C VAL* 3.6 15.3 - - + -
195C TYR* 2.6 36.9 + - + +
196C THR* 4.1 12.8 - - - -
199C ALA* 3.6 12.0 - - + -
200C SER* 2.7 40.8 + - - -
315C SER* 4.9 0.7 - - - -
319C THR* 3.6 24.6 - - + +
323C LEU* 4.8 0.2 - - - -
455C LEU* 3.0 39.7 + - + +
456C ALA* 3.8 3.8 - - - +
458C ALA* 1.3 75.2 - - - +
460C MET* 1.3 63.1 + - - +
463C LEU* 3.3 9.2 + - - +
601C HEM 6.3 0.9 - - - -
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Residues in contact with MET 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C THR* 3.7 21.8 - - + +
322C PRO* 3.2 39.0 - - + +
323C LEU* 3.3 32.4 - - + +
326C THR* 4.5 1.1 - - - +
369C LEU* 4.0 32.1 - - + -
372C THR* 5.4 1.1 - - + -
373C LEU* 5.5 6.1 - - + -
443C PHE* 6.1 0.7 - - - -
456C ALA 3.2 14.9 + - - +
457C GLU* 3.7 7.4 - - - +
459C GLU* 1.3 75.3 - - - +
461C LEU* 1.3 65.3 + - - +
463C LEU 3.3 1.6 + - - -
464C LEU* 3.1 30.2 + - - +
601C HEM 4.4 16.6 - - - -
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Residues in contact with LEU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 5.6 0.9 - - + -
358C ALA* 3.7 38.6 - - + +
359C THR* 4.2 9.2 - - + +
362C LEU* 4.2 10.5 - - + +
365C LEU* 3.4 36.0 - - + +
366C ARG* 3.6 36.1 - - + +
369C LEU* 4.1 8.7 - - + +
457C GLU* 2.8 18.3 + - + +
458C ALA* 3.8 8.3 - - - +
460C MET* 1.3 77.9 - - - +
462C LEU* 1.3 58.5 + - + +
464C LEU* 3.4 1.3 + - - -
465C HIS* 2.8 29.0 + - - +
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Residues in contact with LEU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 2.9 36.1 - - + +
161C VAL* 3.9 16.2 - - + -
162C ASP* 3.9 31.9 - - + +
165C ALA* 3.6 14.8 - - + -
351C ILE* 4.7 4.3 - - + -
355C PRO 4.8 2.2 - - - +
358C ALA* 3.8 23.8 - - + -
458C ALA 3.1 15.7 + - - +
459C GLU 4.4 1.1 - - - +
461C LEU* 1.3 79.9 - - + +
463C LEU* 1.3 66.5 + - - +
465C HIS* 3.7 11.6 - - + +
466C HIS* 3.0 38.1 + - + -
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Residues in contact with LEU 463 (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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165C ALA* 3.8 10.1 - - - +
168C PHE* 3.8 27.6 - - + -
192C ILE* 3.8 25.8 - - + -
195C TYR* 3.4 44.0 - - + +
323C LEU* 3.8 18.6 - - + -
327C LEU* 4.9 4.9 - - + -
459C GLU 3.3 17.9 + - - +
460C MET 3.3 3.9 + - - +
462C LEU* 1.3 76.5 - - - +
464C LEU* 1.3 72.6 + - + +
466C HIS* 3.2 3.6 + - - +
467C VAL* 3.0 33.4 + - + +
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Residues in contact with LEU 464 (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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323C LEU* 3.7 19.1 - - + -
326C THR* 3.8 24.7 - - + -
327C LEU* 3.8 28.9 - - + -
330C LEU* 4.5 10.5 - - + -
365C LEU* 3.9 21.1 - - + -
369C LEU* 3.7 29.2 - - + -
460C MET 3.1 18.9 + - - +
461C LEU* 3.7 4.0 - - - +
463C LEU* 1.3 78.9 - - + +
465C HIS* 1.3 63.1 + - - +
467C VAL* 3.1 4.5 + - + +
468C LEU* 2.8 31.4 + - + +
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Residues in contact with HIS 465 (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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344C SER* 3.1 46.3 + - - -
348C ALA* 4.3 3.7 - - - -
351C ILE* 3.4 40.9 - - + +
362C LEU* 3.6 20.2 - - + +
365C LEU* 3.7 6.2 - - - +
461C LEU 2.8 18.7 + - - +
462C LEU* 3.7 9.4 - - + +
463C LEU 3.2 0.2 - - - -
464C LEU* 1.3 76.0 - - - +
466C HIS* 1.3 88.3 + + - +
468C LEU* 3.6 2.1 + - - +
469C LYS* 3.2 42.4 + - + +
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Residues in contact with HIS 466 (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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162C ASP* 2.9 39.6 + - - -
165C ALA* 3.8 24.5 - - + +
166C ARG* 3.6 28.2 + - + -
169C SER* 3.2 12.9 + - - +
351C ILE* 5.4 1.6 - - - +
462C LEU* 3.0 30.2 + - + +
463C LEU 3.2 1.5 + - - +
465C HIS* 1.3 94.4 + + - +
467C VAL* 1.3 63.4 + - - +
469C LYS* 3.6 25.6 + - + +
470C HIS* 3.0 33.5 + + - +
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Residues in contact with VAL 467 (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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168C PHE* 4.3 17.7 - - + -
169C SER* 3.5 14.4 - - - +
327C LEU* 4.5 10.3 - - + -
463C LEU* 3.0 34.5 + - + +
464C LEU* 3.1 6.5 + - + +
466C HIS* 1.3 76.6 - - - +
468C LEU* 1.3 58.7 + - + +
470C HIS 3.0 1.2 + - - -
471C PHE* 2.7 49.5 + - + +
473C VAL* 4.1 16.6 - - + -
499C PHE* 3.9 23.3 - - + -
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Residues in contact with LEU 468 (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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330C LEU* 4.3 13.7 - - + -
337C GLN* 3.8 37.9 - - + +
340C LEU* 3.8 30.7 - - + +
341C ARG* 3.2 44.5 + - - +
344C SER* 4.1 12.6 - - - +
365C LEU* 4.1 19.1 - - + -
464C LEU* 2.8 23.7 + - + +
465C HIS 3.9 3.1 - - - +
467C VAL* 1.3 80.0 - - + +
469C LYS* 1.3 62.0 + - - +
470C HIS 3.2 0.3 + - - -
471C PHE 4.2 4.3 - - - +
473C VAL* 5.9 2.0 - - + -
502C ILE* 3.7 2.3 - - - +
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Residues in contact with LYS 469 (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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166C ARG* 4.2 4.8 - - - +
344C SER* 4.1 17.9 - - - +
345C LEU* 3.9 26.5 - - + +
348C ALA* 4.0 17.9 + - + +
352C SER* 4.0 18.8 + - - -
465C HIS* 3.2 42.0 + - + +
466C HIS* 3.7 29.2 + - + +
467C VAL 3.3 0.4 - - - -
468C LEU* 1.3 76.2 - - - +
470C HIS* 1.3 80.9 + - + +
502C ILE* 3.3 14.1 - - - +
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Residues in contact with HIS 470 (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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169C SER* 4.2 12.9 - - - -
170C GLN* 6.5 0.2 - - - -
173C LYS* 3.3 40.8 + - + +
466C HIS* 3.0 24.8 + + - +
467C VAL 3.0 2.2 + - - -
469C LYS* 1.3 104.7 - - + +
471C PHE* 1.3 81.9 + + + +
501C ALA* 3.5 7.4 - - - -
502C ILE* 3.1 27.0 + - - -
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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
------------------------------------------------------------
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