Contacts of the helix formed by residues 451 - 462 (chain B) in PDB entry 6FEQ
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 GLU 451 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B MET* 4.8 5.8 - - - +
383B ARG* 4.6 4.6 + - - -
387B ASN* 3.9 19.6 + - - +
447B LEU* 3.9 18.0 + - + +
448B PHE 4.2 3.8 + - - +
449B VAL 3.3 0.4 - - - -
450B VAL* 1.3 85.4 - - + +
452B LYS* 1.3 57.9 + - - +
453B LYS 3.5 1.3 - - - -
454B LEU* 3.3 36.7 + - - +
455B PHE* 2.9 27.9 + - - +
469B TYR* 3.9 16.3 + - - +
473B LYS* 4.3 16.9 + - - +
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Residues in contact with LYS 452 (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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448B PHE 3.6 14.0 + - - +
449B VAL 3.3 15.0 + - - +
450B VAL 3.2 4.0 - - - -
451B GLU* 1.3 77.2 - - - +
453B LYS* 1.3 64.1 + - + +
455B PHE* 3.1 9.6 + - + +
456B ILE* 3.0 53.8 + - + +
530B GLY* 2.4 37.7 + - - +
531B GLN 3.3 23.5 - - - +
532B SER* 3.6 19.3 - - - +
651B LEU* 4.4 14.6 - - + +
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Residues in contact with LYS 453 (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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125B VAL* 4.8 13.1 - - + +
127B ASP* 3.8 31.1 + - - +
129B VAL* 4.7 10.8 - - + +
450B VAL 4.7 2.4 + - - +
451B GLU 3.5 0.2 - - - -
452B LYS* 1.3 79.0 - - + +
454B LEU* 1.3 63.6 + - - +
456B ILE* 4.2 10.8 - - + +
457B HIS* 3.3 25.1 + - - +
532B SER* 6.1 1.1 - - - +
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Residues in contact with LEU 454 (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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129B VAL* 3.3 46.3 - - + +
131B MET* 4.0 8.5 - - + -
198B MET* 5.9 3.8 - - + -
383B ARG* 3.8 25.1 - - - +
450B VAL 5.4 0.4 + - - -
451B GLU* 3.3 32.6 + - - +
452B LYS 3.2 0.8 - - - -
453B LYS* 1.3 78.4 - - - +
455B PHE* 1.3 62.1 + - - +
457B HIS* 4.1 2.8 - - + +
458B GLU* 3.2 60.9 + - + +
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Residues in contact with PHE 455 (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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451B GLU 2.9 14.7 + - - +
452B LYS* 3.3 12.6 - - + +
454B LEU* 1.3 78.5 - - - +
456B ILE* 1.3 71.9 + - + +
458B GLU* 4.8 0.2 - - - -
459B TYR* 3.1 27.8 + - + +
464B TYR* 4.0 15.1 + + - -
466B VAL* 4.1 33.4 - - + -
469B TYR* 3.4 59.2 + + + +
648B LEU* 4.0 26.5 - - + -
651B LEU* 4.8 5.4 - - + -
653B LYS* 4.2 20.9 - - - -
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Residues in contact with ILE 456 (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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452B LYS* 3.0 43.3 + - + +
453B LYS* 4.2 10.1 - - + +
455B PHE* 1.3 88.4 - - + +
457B HIS* 1.3 65.7 + - - +
459B TYR* 3.4 3.2 + - - +
460B ILE* 3.2 30.1 + - + +
651B LEU* 4.4 13.5 - - + -
652B LYS 5.1 6.5 - - - +
653B LYS* 3.5 33.2 - - + +
654B TYR 6.0 0.9 - - - -
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Residues in contact with HIS 457 (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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96B ARG* 3.3 34.3 + - - +
123B TYR* 3.0 34.8 + + - +
124B VAL* 5.4 0.2 - - - -
125B VAL* 3.6 24.7 - - + +
129B VAL* 5.1 9.9 - - + +
199B GLU* 3.3 26.5 - - - -
453B LYS 3.3 16.8 + - - +
454B LEU* 4.3 3.7 - - + +
456B ILE* 1.3 80.0 - - - +
458B GLU* 1.3 66.6 + - - +
460B ILE* 4.2 2.0 - - - +
461B SER* 2.9 40.5 + - - -
463B TYR* 4.9 2.6 + - - -
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Residues in contact with GLU 458 (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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142B PHE* 3.9 14.4 - - - -
198B MET* 5.3 4.3 - - - +
383B ARG* 4.5 7.6 + - - -
454B LEU* 3.2 46.8 + - + +
455B PHE 4.1 0.2 - - - +
457B HIS* 1.3 83.8 - - - +
459B TYR* 1.3 53.1 + - - +
461B SER* 3.1 6.8 + - - -
462B GLY 2.4 31.4 + - - -
463B TYR* 3.2 42.5 + - + -
464B TYR* 2.5 44.8 + - + +
469B TYR* 5.1 0.3 - - - -
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Residues in contact with TYR 459 (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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369B TYR* 3.6 25.0 + + - -
455B PHE* 3.1 28.8 + - + +
456B ILE* 3.4 4.2 + - - +
458B GLU* 1.3 73.4 - - - +
460B ILE* 1.3 68.2 + - + +
462B GLY* 3.1 12.6 + - - +
463B TYR 4.9 0.7 - - - +
464B TYR* 3.6 29.8 + + + -
465B ARG 4.8 0.4 - - - -
466B VAL* 3.6 28.4 - - + +
649B LEU* 5.4 5.2 - - + +
653B LYS* 3.3 41.1 - - + -
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Residues in contact with ILE 460 (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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96B ARG* 3.4 50.5 - - - +
118B LYS* 3.7 47.7 - - + +
119B CYS* 5.7 0.3 - - - -
456B ILE* 3.2 24.2 + - + +
457B HIS* 4.2 0.9 - - - +
459B TYR* 1.3 79.1 - - + +
461B SER* 1.3 60.4 + - - +
462B GLY* 3.4 1.2 + - - -
653B LYS* 3.4 32.1 - - + +
654B TYR* 4.3 15.3 - - + -
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 3.6 14.9 + - - +
118B LYS 4.2 13.3 + - - +
119B CYS* 4.0 18.6 - - - -
147B ARG* 5.6 3.9 + - - +
199B GLU* 4.6 6.8 + - - -
457B HIS* 2.9 31.5 + - - -
458B GLU* 3.1 5.5 + - - -
460B ILE* 1.3 76.0 - - - +
462B GLY* 1.3 63.4 + - - +
463B TYR* 3.6 27.3 - - - -
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Residues in contact with GLY 462 (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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119B CYS* 5.2 5.6 - - - -
146B LEU 4.6 4.2 - - - +
147B ARG* 5.9 0.2 - - - +
369B TYR* 5.0 13.9 - - - +
370B THR* 5.1 8.7 + - - -
458B GLU 2.4 14.6 + - - -
459B TYR* 3.1 15.9 + - - -
460B ILE 4.2 1.1 - - - -
461B SER* 1.3 77.7 - - - +
463B TYR* 1.3 63.0 + - - -
464B TYR 3.2 9.0 - - - -
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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