Contacts of the helix formed by residues 418 - 431 (chain B) in PDB entry 3OFN
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 GLN 418 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B ALA 4.6 2.2 + - - +
415B SER 3.6 10.7 + - - +
416B THR 3.1 1.2 - - - -
417B LYS* 1.3 76.0 - - - +
419B THR* 1.3 61.9 + - + +
420B LEU 3.1 1.3 - - - -
421B VAL* 3.3 10.1 + - + +
422B ARG* 3.1 33.0 + - + +
456B ASP* 3.9 19.2 + - - +
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Residues in contact with THR 419 (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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395B PHE* 3.8 22.6 - - + -
399B TYR* 3.7 11.2 - - - -
402B VAL* 4.4 12.0 - - - +
415B SER 5.5 0.4 - - - +
416B THR* 2.7 36.6 + - + +
418B GLN* 1.3 78.2 - - + +
420B LEU* 1.3 58.1 + - - +
421B VAL 3.3 0.2 - - - -
422B ARG* 3.7 9.0 - - + +
423B GLY* 2.9 25.5 + - - -
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B TYR* 4.1 9.6 - - + -
402B VAL* 4.1 17.0 - - + -
403B ALA* 3.9 35.4 - - + -
406B ALA* 4.5 14.6 - - + -
416B THR 3.3 3.3 + - - +
417B LYS* 3.3 32.3 - - + +
419B THR* 1.3 81.3 + - - +
421B VAL* 1.3 61.2 + - + +
423B GLY 4.1 0.4 - - - -
424B GLU* 3.5 36.8 + - - +
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Residues in contact with VAL 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LYS* 3.2 19.1 - - + +
418B GLN* 3.3 12.3 + - + +
419B THR 3.3 0.2 - - - -
420B LEU* 1.3 75.9 - - + +
422B ARG* 1.3 65.5 + - - +
424B GLU* 3.2 2.5 + - - -
425B ARG* 2.9 64.4 + - + +
456B ASP* 3.9 23.3 - - + +
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Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.7 20.8 - - + -
418B GLN* 3.1 22.6 + - + +
419B THR* 3.7 4.5 - - + +
421B VAL* 1.3 75.0 - - - +
423B GLY* 1.3 53.0 + - - +
425B ARG* 3.1 6.0 + - - +
426B LEU* 2.7 48.9 + - - +
450B GLY 4.0 13.5 - - - -
451B VAL 3.8 13.0 + - - -
452B ASN 3.2 10.1 + - - -
453B GLY* 3.1 28.9 + - - -
456B ASP* 2.8 36.1 + - - +
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Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 4.1 7.2 - - - -
396B LEU* 4.8 0.3 - - - +
399B TYR* 3.5 35.6 - - - -
419B THR 2.9 16.1 + - - -
421B VAL 3.2 0.2 - - - -
422B ARG* 1.3 77.5 - - - +
424B GLU* 1.3 53.2 + - - +
426B LEU* 3.0 2.2 + - - +
427B THR* 2.6 36.9 + - - -
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B TYR* 3.5 18.2 + - - +
420B LEU* 3.5 30.4 + - - +
421B VAL* 3.2 5.1 + - - +
423B GLY* 1.3 73.6 - - - +
425B ARG* 1.3 62.3 + - - +
427B THR* 3.7 5.9 - - + -
428B GLN* 3.1 23.6 + - - +
460B LEU* 3.3 40.8 - - + +
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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
----------------------------------------------------------
421B VAL* 2.9 57.8 + - + +
422B ARG* 3.4 9.2 - - - +
424B GLU* 1.3 82.6 + - - +
426B LEU* 1.3 59.6 + - + +
428B GLN* 3.2 5.2 + - - +
429B LEU* 3.0 26.9 + - - +
450B GLY* 6.3 0.2 - - - -
455B LEU* 3.4 39.8 + - + +
456B ASP* 4.2 9.9 + - - +
457B GLY 4.8 2.4 + - - -
458B ILE 2.8 27.0 + - - -
459B GLU* 4.7 1.6 - - - +
460B LEU* 3.3 41.9 - - - +
463B ILE* 3.8 13.6 - - + +
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Residues in contact with LEU 426 (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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392B LEU* 3.7 23.8 - - + -
395B PHE* 3.4 34.8 - - + -
396B LEU* 4.3 13.0 - - + -
422B ARG* 2.7 35.1 + - - +
423B GLY 3.7 2.2 - - - +
425B ARG* 1.3 69.9 - - + +
427B THR* 1.3 66.1 + - - +
429B LEU* 3.2 12.4 + - + +
430B LEU* 3.1 32.8 + - + +
447B ILE* 5.1 1.6 - - + +
450B GLY* 3.6 36.3 - - - +
451B VAL* 3.8 7.6 - - + +
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ILE* 4.2 31.7 - - + +
396B LEU* 4.7 6.5 - - - +
399B TYR* 3.4 22.5 + - - +
400B ARG* 5.9 1.0 - - - -
423B GLY 2.6 22.0 + - - -
424B GLU* 3.7 10.3 - - + +
426B LEU* 1.3 74.1 - - - +
428B GLN* 1.3 64.9 + - + +
429B LEU 3.3 0.2 + - - -
430B LEU* 3.4 10.7 + - - +
431B LYS* 3.3 28.7 + - - +
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Residues in contact with GLN 428 (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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153B LYS* 5.1 0.2 + - - -
424B GLU 3.1 16.1 + - - +
425B ARG 3.2 10.1 + - - +
427B THR* 1.3 80.5 - - + +
429B LEU* 1.3 63.8 + - - +
431B LYS* 2.9 56.1 + - - +
460B LEU* 3.5 39.4 + - + +
463B ILE* 3.8 20.9 - - + +
464B GLY 5.5 2.9 + - - +
467B GLU* 5.6 0.3 - - - +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 2.7 35.7 + - + +
425B ARG 3.0 15.6 + - - +
426B LEU* 3.2 14.1 + - + +
428B GLN* 1.3 79.0 - - - +
430B LEU* 1.3 55.8 + - + +
446B LEU* 3.2 54.3 - - + +
447B ILE* 4.2 11.0 - - + +
450B GLY* 4.1 9.9 - - - -
455B LEU* 4.0 16.8 - - + -
463B ILE* 4.5 17.9 - - + +
466B PHE* 5.4 2.9 - - + -
467B GLU* 4.1 15.8 - - + +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 3.7 24.6 - - + +
154B ALA* 3.8 36.0 + - + +
157B ALA* 4.6 9.6 - - + -
158B LEU* 4.3 8.5 - - + -
365B PRO* 4.1 9.0 - - - +
392B LEU* 4.6 13.0 - - + -
396B LEU* 3.8 30.7 - - + -
426B LEU* 3.1 22.6 + - + +
427B THR* 4.1 5.2 - - - +
428B GLN 3.3 0.2 - - - -
429B LEU* 1.3 77.7 - - + +
431B LYS* 1.3 68.7 + - - +
432B GLN* 3.4 7.8 + - - +
447B ILE* 5.1 7.6 - - + -
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Residues in contact with LYS 431 (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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153B LYS* 2.6 32.2 + - - -
361B LYS 5.0 3.2 + - - -
362B GLY* 4.2 17.8 + - - +
363B ILE* 3.9 37.0 - - + +
364B ARG 3.7 11.0 - - - +
365B PRO* 4.8 0.2 - - - -
427B THR* 3.3 22.9 + - - +
428B GLN* 2.9 47.0 + - - +
429B LEU 3.6 0.7 - - - +
430B LEU* 1.3 75.1 - - - +
432B GLN* 1.3 53.6 + - - +
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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
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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