Contacts of the helix formed by residues 416 - 429 (chain A) in PDB entry 3F7F
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 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASN* 6.1 1.3 - - - -
13A GLN* 4.4 25.1 - - - -
412A LYS 3.0 17.6 + - - -
413A SER 4.0 2.7 + - - -
414A ARG 3.7 1.2 - - - -
415A TYR* 1.3 80.6 - - - +
417A THR* 1.3 61.6 + - - -
418A GLN* 3.4 2.5 - - - -
419A ILE 3.4 1.7 + - - -
420A PHE* 3.0 26.7 + - - +
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Residues in contact with THR 417 (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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12A LEU 5.5 2.0 + - - -
13A GLN* 5.1 1.4 + - - +
15A TYR 3.7 15.3 + - - -
16A GLU* 2.8 36.0 + - - +
18A PRO* 3.2 23.8 - - + -
412A LYS* 3.7 19.2 + - - +
416A GLY* 1.3 67.9 - - - -
418A GLN* 1.3 65.6 + - - +
420A PHE* 4.4 5.8 - - - -
421A GLU* 3.0 43.0 + - + +
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Residues in contact with GLN 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 3.0 33.9 + - - +
12A LEU* 5.0 8.0 + - + +
18A PRO* 3.4 31.3 + - + +
416A GLY 3.4 0.8 - - - -
417A THR* 1.3 79.2 - - - +
419A ILE* 1.3 61.0 + - - +
421A GLU* 4.2 1.4 - - - +
422A ARG* 3.3 21.1 + - - +
457A PHE* 3.4 17.5 - - + -
477A GLN* 3.5 17.7 - - - +
478A PRO* 3.2 22.6 + - - +
479A TYR* 3.8 15.8 - - - +
480A ASN* 3.1 10.4 + - - -
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 4.4 15.5 - - + +
415A TYR* 3.6 38.1 - - + +
416A GLY 3.4 6.3 + - - +
417A THR 3.2 0.2 - - - -
418A GLN* 1.3 74.8 - - - +
420A PHE* 1.3 67.9 + - - +
422A ARG* 3.0 4.6 + - - +
423A ALA* 2.9 21.3 + - - +
450A LEU* 4.1 17.0 - - + +
453A VAL* 3.9 15.0 - - + +
454A LYS* 3.8 33.9 - - + +
457A PHE* 3.5 30.7 - - + -
480A ASN* 4.7 2.7 - - - +
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Residues in contact with PHE 420 (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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408A PHE* 3.6 35.7 - + - -
411A LEU* 4.2 10.1 - - + -
412A LYS* 3.7 60.6 - - + -
415A TYR* 4.6 1.5 - - + +
416A GLY 3.0 20.6 + - - +
417A THR* 4.0 4.3 - - - +
419A ILE* 1.3 76.6 - - - +
421A GLU* 1.3 62.6 + - + +
423A ALA* 3.1 5.5 + - - +
424A GLN* 3.0 49.9 + - - +
446A LEU* 4.0 20.2 - - + -
450A LEU* 3.6 23.1 - - + +
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Residues in contact with GLU 421 (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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16A GLU 5.0 0.2 - - - +
17A LYS* 4.9 6.3 + - - -
18A PRO* 3.2 25.4 - - + +
412A LYS* 5.0 6.8 + - - +
417A THR* 3.0 33.9 + - + +
418A GLN 4.4 1.3 - - - +
420A PHE* 1.3 84.9 - - + +
422A ARG* 1.3 61.4 + - - +
424A GLN* 3.9 10.9 - - - +
425A GLN* 3.1 21.7 + - - +
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Residues in contact with ARG 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLN 3.3 19.0 + - - +
419A ILE 3.0 6.1 + - - +
421A GLU* 1.3 77.4 - - - +
423A ALA* 1.3 58.1 + - - +
424A GLN 3.4 0.2 - - - -
425A GLN* 3.3 26.4 + - - +
426A ILE* 3.2 40.6 + - - +
453A VAL* 3.7 20.3 - - + +
457A PHE* 3.9 27.8 - - + -
477A GLN* 5.0 7.9 + - - +
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Residues in contact with ALA 423 (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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419A ILE 2.9 6.0 + - - +
420A PHE 3.1 8.5 + - - +
422A ARG* 1.3 75.2 - - - +
424A GLN* 1.3 61.7 + - - +
425A GLN 3.0 5.2 - - - -
426A ILE 3.5 1.2 + - - -
427A LEU* 3.1 28.4 + - - +
446A LEU* 4.0 7.4 - - + -
449A ILE* 3.4 29.7 - - + +
450A LEU* 3.5 29.6 - - + +
453A VAL* 4.2 3.8 - - + -
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Residues in contact with GLN 424 (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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408A PHE* 3.3 31.1 - - - -
420A PHE* 3.0 38.7 + - + +
421A GLU* 3.4 10.6 + - - +
422A ARG 3.4 0.2 - - - -
423A ALA* 1.3 77.0 - - - +
425A GLN* 1.3 62.0 + - - +
427A LEU* 3.7 8.5 - - - +
428A SER* 3.3 20.8 + - - -
442A TYR* 3.6 19.0 + - - +
446A LEU* 4.3 12.8 - - + -
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Residues in contact with GLN 425 (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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421A GLU 3.1 13.9 + - - +
422A ARG* 3.3 35.9 + - - +
424A GLN* 1.3 75.8 - - - +
426A ILE* 1.3 68.4 + - - +
427A LEU 2.9 5.5 + - - -
428A SER* 3.0 19.6 + - - +
429A GLU* 3.0 35.9 + - + +
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Residues in contact with ILE 426 (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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422A ARG* 3.2 41.9 + - - +
423A ALA 3.9 4.7 - - - +
425A GLN* 1.3 79.7 - - - +
427A LEU* 1.3 58.8 + - - +
429A GLU* 4.1 12.1 - - - +
430A ASN* 3.0 33.7 + - - +
432A ILE* 5.3 0.3 - - - +
449A ILE* 4.3 23.8 - - + -
453A VAL* 4.1 16.2 - - + -
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Residues in contact with LEU 427 (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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423A ALA 3.1 18.5 + - - +
424A GLN* 3.7 10.1 - - + +
425A GLN 2.9 1.0 - - - -
426A ILE* 1.3 76.2 - - - +
428A SER* 1.3 61.0 + - - +
430A ASN* 3.1 7.8 + - - -
432A ILE* 2.8 73.5 + - + +
442A TYR* 3.2 36.1 - - + +
445A ASN* 4.0 16.2 - - + -
446A LEU* 3.7 28.5 - - + +
449A ILE* 4.5 13.9 - - + -
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLN 3.3 10.9 + - - -
425A GLN* 3.0 17.2 + - - +
427A LEU* 1.3 73.1 - - - +
429A GLU* 1.3 55.8 + - - +
430A ASN 2.9 5.2 - - - -
431A LYS* 2.6 35.2 + - - +
432A ILE 4.0 7.1 + - - +
433A ILE* 4.8 11.6 - - - +
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Residues in contact with GLU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLN* 3.0 47.0 + - + +
426A ILE* 4.1 7.2 - - - +
428A SER* 1.3 79.5 + - - +
430A ASN* 1.3 71.0 + - - +
431A LYS* 3.3 8.8 + - - +
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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