Contacts of the helix formed by residues 518 - 530 (chain A) in PDB entry 1QF6
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 MET 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A PHE* 3.5 46.7 - - + +
277A LEU* 3.2 46.4 - - + -
278A GLU* 4.2 4.7 - - - +
281A VAL* 4.9 0.4 - - - -
358A PHE* 4.6 15.3 - - + -
380A THR* 2.6 28.7 + - + +
382A ASP* 4.6 13.5 - - + -
515A LEU* 3.8 20.6 - - + -
516A GLY 4.2 0.2 + - - -
517A SER* 1.3 71.7 - - - +
519A GLU* 1.3 66.4 + - - +
521A PHE* 3.3 4.5 + - - +
522A ILE* 3.1 30.4 + - - +
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Residues in contact with GLU 519 (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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264A VAL* 5.1 5.4 - - + +
266A TRP* 3.9 37.0 + - + -
274A PHE* 4.0 4.8 - - - -
373A LEU* 3.5 25.8 - - + +
376A VAL* 3.9 13.0 - - + -
378A GLY 4.1 2.4 - - - +
379A PHE* 3.4 25.1 - - + -
380A THR* 2.5 47.4 + - - +
517A SER* 3.8 3.1 - - - +
518A MET* 1.3 74.0 + - - +
520A ARG* 1.3 61.7 + - - +
521A PHE 3.1 0.3 + - - -
522A ILE* 3.1 4.2 + - - +
523A GLY 2.9 17.7 + - - -
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Residues in contact with ARG 520 (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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373A LEU 3.3 10.6 + - - -
374A MET* 2.8 43.2 + - - +
375A ARG* 3.9 18.2 - - - +
478A TRP* 4.0 26.9 - - + -
479A GLN* 2.8 51.3 + - - +
480A CYS* 4.3 9.6 - - - -
515A LEU 5.9 0.2 - - - +
517A SER* 2.9 21.8 + - - +
519A GLU* 1.3 77.3 - - - +
521A PHE* 1.3 62.1 + - - +
523A GLY* 3.3 1.1 + - - +
524A ILE* 3.1 23.8 + - + +
1002A AMP 3.2 38.2 + - - -
75B C 4.8 7.9 + - - -
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Residues in contact with PHE 521 (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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277A LEU* 4.3 7.2 - - + -
408A TYR* 4.0 16.6 - + - -
411A PHE* 3.6 29.6 - + - -
413A PHE* 3.4 34.8 - + - -
470A LEU* 3.9 16.2 - - + -
480A CYS* 4.6 3.6 - - - -
515A LEU* 3.7 49.8 + - + +
517A SER 3.1 16.7 + - - +
518A MET* 3.9 5.4 - - - +
519A GLU 3.1 0.4 - - - -
520A ARG* 1.3 74.3 - - - +
522A ILE* 1.3 56.0 + - + +
523A GLY 3.0 1.3 - - - -
524A ILE* 2.9 8.6 + - + +
525A LEU* 2.7 59.9 + - + +
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Residues in contact with ILE 522 (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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253A LEU* 5.6 4.5 - - + -
266A TRP* 3.8 33.2 - - + -
273A ILE* 4.1 20.4 - - + -
274A PHE* 3.8 31.6 - - + +
277A LEU* 3.5 29.8 - - + -
373A LEU* 4.2 7.4 - - + +
518A MET 3.1 17.9 + - - +
519A GLU 3.6 3.8 - - - +
521A PHE* 1.3 73.1 - - - +
523A GLY* 1.3 66.7 + - - +
525A LEU* 4.4 7.9 - - + +
526A THR* 3.0 37.8 + - - +
533A PHE* 5.5 0.9 - - + -
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Residues in contact with GLY 523 (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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244A HIS* 3.7 9.3 - - - +
373A LEU* 4.0 14.3 - - - +
374A MET* 3.6 19.5 - - - -
519A GLU 2.9 13.7 + - - -
520A ARG 3.6 4.5 - - - -
521A PHE 3.0 0.4 - - - -
522A ILE* 1.3 82.6 - - - +
524A ILE* 1.3 60.2 + - - +
526A THR* 3.7 2.8 - - - -
527A GLU* 3.4 25.5 + - - +
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Residues in contact with ILE 524 (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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374A MET* 3.7 21.8 - - + -
413A PHE* 4.3 16.6 - - + -
470A LEU* 4.2 29.6 - - + -
471A TYR 3.8 31.5 - - - +
472A ASP* 4.4 2.0 - - + -
478A TRP* 4.1 16.2 - - + -
480A CYS* 4.8 6.1 - - - -
520A ARG* 3.1 18.8 + - + +
521A PHE* 2.9 11.6 + - + +
523A GLY* 1.3 73.7 - - - +
525A LEU* 1.3 65.5 + - + +
527A GLU* 3.3 4.4 + - - +
528A GLU* 3.0 21.1 + - + +
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Residues in contact with LEU 525 (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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273A ILE* 5.4 2.7 - - + -
277A LEU* 4.2 17.7 - - + -
411A PHE* 3.5 24.9 - - + -
413A PHE* 3.5 32.1 - - + -
521A PHE* 2.7 32.6 + - + +
522A ILE* 4.0 6.3 - - - +
524A ILE* 1.3 70.7 - - - +
526A THR* 1.3 67.5 + - - +
528A GLU* 3.0 4.6 + - - +
529A PHE* 2.8 41.1 + - + -
533A PHE* 4.2 7.6 - - + -
537A LEU* 3.4 32.1 - - + -
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Residues in contact with THR 526 (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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244A HIS* 3.6 29.6 - - + +
247A ILE* 3.8 27.5 - - + +
248A GLY 4.9 1.6 - - - +
253A LEU* 4.3 7.5 - - + +
373A LEU* 5.7 0.7 - - - +
522A ILE* 3.0 22.7 + - - +
523A GLY 3.7 4.3 - - - -
525A LEU* 1.3 79.6 - - - +
527A GLU* 1.3 59.0 + - - +
530A ALA* 2.8 25.1 + - - -
531A GLY 3.0 9.1 + - - +
533A PHE* 3.0 28.9 - - + -
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Residues in contact with GLU 527 (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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242A ARG* 2.4 45.9 + - - +
243A ASP* 3.1 13.4 - - - +
244A HIS* 2.6 49.2 + - + +
374A MET* 4.3 2.5 - - + -
472A ASP* 3.3 16.1 - - - +
473A CYS* 2.8 56.7 + - + +
523A GLY 3.4 13.2 + - - +
524A ILE* 3.3 7.2 + - - +
525A LEU 3.2 0.4 - - - -
526A THR* 1.3 74.0 - - - +
528A GLU* 1.3 55.0 + - - +
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Residues in contact with GLU 528 (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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242A ARG* 3.2 16.7 + - - +
411A PHE 4.0 11.1 - - - +
412A GLY 4.0 10.9 - - - +
413A PHE* 4.0 27.0 - - + -
414A GLU* 5.4 2.8 + - - +
524A ILE* 3.0 19.0 + - + +
525A LEU* 3.0 7.6 + - - +
527A GLU* 1.3 77.2 - - - +
529A PHE* 1.3 83.3 + - + +
530A ALA 3.3 0.2 - - - -
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Residues in contact with PHE 529 (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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242A ARG* 4.9 0.7 - - - -
411A PHE* 4.0 33.2 - + + -
525A LEU* 2.8 44.9 + - + +
528A GLU* 1.3 95.6 - - + +
530A ALA* 1.3 62.2 + - - +
531A GLY 3.1 1.3 - - - +
532A PHE* 2.7 55.0 + - - +
533A PHE* 3.9 11.0 - + + +
534A PRO* 3.6 36.8 - - + -
537A LEU* 4.5 1.3 - - + -
612A ARG* 5.4 0.2 + - - -
637A LEU* 4.3 11.0 - - + -
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Residues in contact with ALA 530 (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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241A LYS 5.6 0.9 - - - +
242A ARG* 3.3 41.1 - - + +
247A ILE* 3.5 19.0 - - + +
526A THR 2.8 12.2 + - - -
527A GLU 4.1 0.7 - - - -
528A GLU 3.3 3.2 - - - -
529A PHE* 1.3 79.4 - - - +
531A GLY* 1.3 55.8 + - - +
532A PHE* 3.1 24.9 + - + -
589A ARG* 4.2 3.5 + - - -
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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