Contacts of the helix formed by residues 419 - 430 (chain B) in PDB entry 4U7D
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 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B GLN* 4.5 3.4 - - - -
293B LYS* 3.7 14.5 - - - +
391B MET* 4.0 5.9 - - - +
417B TYR 3.6 5.1 + - - -
418B TYR* 1.3 78.2 - - - +
420B PHE* 1.3 67.4 + - - +
421B GLY 3.2 2.9 - - - -
422B ASP* 2.8 32.6 + - - +
423B ILE 4.0 1.7 + - - -
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Residues in contact with PHE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B GLN* 5.3 1.4 - - - +
418B TYR* 4.3 11.3 + - + -
419B GLY* 1.3 69.4 - - - -
421B GLY* 1.3 65.6 + - - +
422B ASP 3.0 1.4 + - - -
423B ILE* 3.3 27.4 + - + +
424B PHE* 3.7 32.0 - + - -
512B PRO* 4.2 13.7 - - + -
513B LEU* 6.2 0.4 - - - -
516B ILE* 4.7 9.4 - - + -
543B GLU* 2.9 76.2 + - + +
546B ILE* 3.7 24.7 - - + -
547B ALA* 3.8 22.7 - - + -
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Residues in contact with GLY 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B GLY 3.1 1.8 + - - -
420B PHE* 1.3 83.8 - - - +
422B ASP* 1.3 63.3 + - - +
424B PHE* 3.2 22.0 + - - +
425B ARG* 3.4 16.8 + - - +
543B GLU* 5.2 0.4 + - - -
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Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LYS* 3.1 38.4 + - - +
322B PHE* 6.4 0.7 - - + -
390B SER* 4.0 18.3 - - - -
391B MET* 4.2 12.2 + - + -
417B TYR 4.4 0.5 - - - +
419B GLY* 2.8 20.1 + - - +
421B GLY* 1.3 76.8 - - - +
423B ILE* 1.3 65.8 + - - +
425B ARG* 3.3 30.7 + - - +
426B ILE* 3.1 34.6 + - + +
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B MET* 4.0 12.0 - - + +
418B TYR* 4.3 6.7 - - + +
419B GLY 4.5 0.2 - - - +
420B PHE* 3.4 21.1 - - + +
422B ASP* 1.3 78.3 - - - +
424B PHE* 1.3 72.5 + - + +
426B ILE* 4.9 0.4 - - - -
427B SER* 2.7 36.6 + - - -
440B LEU* 3.3 21.8 - - + +
441B TYR* 4.7 4.0 - - + -
444B VAL* 3.7 39.3 - - + -
547B ALA* 4.2 20.4 - - + -
550B LEU* 4.4 13.9 - - + -
551B ILE* 5.8 1.3 - - + -
557B GLU* 4.4 5.4 - - - +
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Residues in contact with PHE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B PHE* 3.7 43.1 - + - -
421B GLY* 3.2 11.3 + - - +
422B ASP 3.1 0.8 - - - -
423B ILE* 1.3 81.9 - - + +
425B ARG* 1.3 64.7 + - + +
427B SER* 4.1 3.8 - - - -
428B SER* 2.6 32.2 + - - -
512B PRO* 3.6 36.3 - - + -
546B ILE* 5.5 0.7 - - + -
550B LEU* 3.8 23.8 - - + -
557B GLU* 3.3 18.2 - - - -
568B SER* 3.8 13.5 - - - -
570B LEU* 3.7 27.1 - - + -
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LYS* 4.9 2.8 - - - +
322B PHE* 3.2 61.2 - - + +
323B SER* 4.1 2.8 + - - -
326B ASP* 2.7 37.2 + - - -
389B HIS* 5.6 0.2 - - - -
390B SER* 3.6 4.6 + - - -
421B GLY 3.5 15.5 - - - +
422B ASP* 3.3 28.2 + - - +
424B PHE* 1.3 80.4 - - - +
426B ILE* 1.3 60.5 + - - +
428B SER* 3.8 3.7 - - - -
429B MET* 3.3 15.6 + - - +
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PHE* 3.4 30.1 - - + -
390B SER* 5.5 0.9 - - - -
391B MET* 3.5 42.2 - - + +
392B SER 4.0 5.2 - - - +
393B LYS* 4.4 15.3 - - + +
422B ASP* 3.1 20.4 + - + +
423B ILE 3.7 2.5 - - - +
425B ARG* 1.3 72.9 - - - +
427B SER* 1.3 66.7 + - - +
428B SER 3.1 1.3 - - - -
429B MET* 2.8 12.3 + - - +
430B VAL* 2.9 30.1 + - + +
440B LEU* 3.5 26.2 - - + -
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B ILE 2.7 21.6 + - - -
424B PHE* 4.1 1.1 - - - -
426B ILE* 1.3 73.3 - - - +
428B SER* 1.3 62.9 + - - +
430B VAL* 3.3 15.0 + - - +
431B VAL* 3.4 7.4 + - - -
437B GLN* 4.0 3.1 + - - +
440B LEU* 3.4 15.4 - - - +
441B TYR* 4.0 5.2 - - - -
557B GLU* 2.5 42.8 + - - -
559B TYR* 2.8 26.2 + - - -
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B PHE 2.6 23.7 + - - -
425B ARG* 3.8 5.4 - - - -
427B SER* 1.3 77.7 - - - +
429B MET* 1.3 60.6 + - - +
431B VAL* 3.3 22.3 - - - +
559B TYR* 3.6 11.2 - - - -
566B THR* 3.2 40.8 + - - +
567B ILE* 3.8 1.2 - - - -
568B SER* 2.7 22.9 + - - -
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Residues in contact with MET 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B PHE* 4.4 13.9 - - + -
425B ARG 3.3 13.4 + - - +
426B ILE* 2.8 13.1 + - - +
428B SER* 1.3 78.0 - - - +
430B VAL* 1.3 60.9 + - + +
431B VAL* 3.2 8.5 + - - +
432B MET* 4.7 4.0 + - - +
433B GLU* 5.3 0.5 - - - +
566B THR* 6.3 1.6 - - - -
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LYS* 3.9 31.0 - - + -
426B ILE* 2.9 30.4 + - + +
427B SER* 3.3 12.5 + - - +
429B MET* 1.3 81.1 - - + +
431B VAL* 1.3 56.0 + - - +
432B MET 3.1 2.7 - - - -
433B GLU* 2.7 55.0 + - - +
436B GLY* 3.6 28.8 - - - +
437B GLN* 4.0 4.3 + - + +
439B LYS* 5.8 0.4 - - - +
440B LEU* 5.1 1.1 - - + -
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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
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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