Contacts of the helix formed by residues 416 - 429 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ASN* 6.1 1.6 - - - -
13B GLN* 4.5 25.1 - - - -
412B LYS 3.0 17.7 + - - -
413B SER 4.0 2.7 + - - -
414B ARG 3.7 1.2 - - - -
415B TYR* 1.3 80.8 - - - +
417B THR* 1.3 61.6 + - - -
418B GLN* 3.4 2.7 - - - -
419B ILE 3.3 1.9 + - - -
420B PHE* 2.9 26.5 + - - +
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Residues in contact with THR 417 (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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12B LEU 5.5 2.0 + - - -
13B GLN* 5.1 1.2 + - - +
15B TYR 3.8 15.5 + - - -
16B GLU* 2.8 34.6 + - - +
18B PRO* 3.2 24.2 - - + -
412B LYS* 3.7 19.3 + - - +
416B GLY* 1.3 68.3 - - - -
418B GLN* 1.3 65.6 + - - +
420B PHE* 4.4 5.8 - - - -
421B GLU* 3.0 43.0 + - + +
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Residues in contact with GLN 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.0 33.4 + - - +
12B LEU* 5.0 7.0 + - + +
18B PRO* 3.4 30.2 + - + +
416B GLY 3.4 1.0 - - - -
417B THR* 1.3 78.8 - - - +
419B ILE* 1.3 60.7 + - - +
421B GLU* 4.2 1.4 - - - +
422B ARG* 3.3 20.8 + - - +
457B PHE* 3.4 17.1 - - + -
477B GLN* 3.5 18.3 - - - +
478B PRO* 3.2 23.0 + - - +
479B TYR* 3.8 15.6 - - - +
480B ASN* 3.1 10.2 + - - -
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 4.4 15.3 - - + +
415B TYR* 3.6 38.4 - - + +
416B GLY 3.3 6.3 + - - +
417B THR 3.2 0.2 - - - -
418B GLN* 1.3 75.2 - - - +
420B PHE* 1.3 67.4 + - - +
422B ARG* 2.9 4.6 + - - +
423B ALA* 2.9 21.1 + - - +
450B LEU* 4.1 16.6 - - + +
453B VAL* 3.8 15.4 - - + +
454B LYS* 3.8 33.7 - - + +
457B PHE* 3.5 32.1 - - + -
480B ASN* 4.6 2.5 - - - +
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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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408B PHE* 3.6 35.2 - + - -
411B LEU* 4.2 10.1 - - + -
412B LYS* 3.7 60.8 - - + -
415B TYR* 4.6 1.5 - - + +
416B GLY 2.9 20.4 + - - +
417B THR* 4.0 4.3 - - - +
419B ILE* 1.3 76.8 - - - +
421B GLU* 1.3 62.9 + - + +
423B ALA* 3.1 5.5 + - - +
424B GLN* 3.0 50.6 + - - +
446B LEU* 3.9 20.4 - - + -
450B LEU* 3.6 22.9 - - + +
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Residues in contact with GLU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU 5.1 0.3 - - - +
17B LYS* 4.9 6.3 + - - -
18B PRO* 3.2 25.8 - - + +
412B LYS* 5.0 6.5 + - - +
417B THR* 3.0 33.8 + - + +
418B GLN 4.4 1.6 - - - +
420B PHE* 1.3 84.2 - - + +
422B ARG* 1.3 61.9 + - - +
424B GLN* 3.9 11.1 - - - +
425B GLN* 3.1 21.7 + - - +
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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
----------------------------------------------------------
418B GLN 3.3 18.8 + - - +
419B ILE 2.9 6.3 + - - +
421B GLU* 1.3 77.2 - - - +
423B ALA* 1.3 58.1 + - - +
425B GLN* 3.3 26.0 + - - +
426B ILE* 3.2 40.8 + - - +
453B VAL* 3.7 20.0 - - + +
457B PHE* 3.9 27.8 - - + -
477B GLN* 5.0 7.9 + - - +
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Residues in contact with ALA 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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419B ILE 2.9 6.2 + - - +
420B PHE 3.1 8.5 + - - +
422B ARG* 1.3 75.7 - - - +
424B GLN* 1.3 61.4 + - - +
425B GLN 3.0 4.9 - - - -
426B ILE 3.5 1.6 + - - -
427B LEU* 3.1 28.3 + - - +
446B LEU* 4.0 6.1 - - + -
449B ILE* 3.4 30.1 - - + +
450B LEU* 3.5 30.3 - - + +
453B VAL* 4.2 3.8 - - + -
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PHE* 3.3 30.9 - - - -
420B PHE* 3.0 40.7 + - + +
421B GLU* 3.4 10.8 + - - +
423B ALA* 1.3 75.9 - - - +
425B GLN* 1.3 63.2 + - - +
427B LEU* 3.7 8.3 - - - +
428B SER* 3.3 20.6 + - - -
442B TYR* 3.6 18.8 + - - +
446B LEU* 4.3 10.5 - - + -
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Residues in contact with GLN 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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421B GLU 3.1 13.9 + - - +
422B ARG* 3.3 35.9 + - - +
424B GLN* 1.3 75.4 - - - +
426B ILE* 1.3 68.6 + - - +
427B LEU 2.9 5.3 + - - -
428B SER* 2.9 19.6 + - - +
429B GLU* 3.0 34.9 + - + +
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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
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422B ARG* 3.2 41.6 + - - +
423B ALA 3.9 4.9 - - - +
425B GLN* 1.3 79.5 - - - +
427B LEU* 1.3 59.4 + - - +
429B GLU* 4.1 11.7 - - - +
430B ASN* 3.0 34.2 + - - +
432B ILE* 5.3 0.3 - - - +
449B ILE* 4.3 22.7 - - + -
453B VAL* 4.1 15.7 - - + -
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Residues in contact with LEU 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 ALA 3.1 21.5 + - - +
424B GLN* 3.7 10.1 - - - +
425B GLN 2.9 1.0 - - - -
426B ILE* 1.3 76.4 - - - +
428B SER* 1.3 65.3 + - - +
430B ASN* 3.1 7.6 + - - -
432B ILE* 2.8 69.9 + - + +
442B TYR* 3.2 35.9 - - + +
445B ASN* 4.0 14.8 - - + -
446B LEU* 3.7 24.9 - - + +
449B ILE* 4.5 14.4 - - + -
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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 GLN 3.3 11.0 + - - -
425B GLN* 2.9 17.5 + - - +
427B LEU* 1.3 73.1 - - - +
429B GLU* 1.3 55.9 + - - +
430B ASN 2.9 4.9 - - - -
431B LYS* 2.7 35.6 + - - +
432B ILE 4.0 7.3 + - - +
433B ILE* 4.8 10.7 - - - +
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Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLN* 3.0 47.0 + - + +
426B ILE* 4.1 7.4 - - - +
428B SER* 1.3 78.9 + - - +
430B ASN* 1.3 70.4 + - - +
431B LYS* 3.3 8.9 + - - +
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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