Contacts of the helix formed by residues 525 - 535 (chain B) in PDB entry 4EG8
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 ILE 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409B LEU* 4.3 4.3 - - + -
416B LEU* 3.8 8.5 - - + +
420B TYR* 3.7 14.6 - - - +
436B VAL* 3.9 9.2 - - + -
439B ALA* 4.3 10.3 - - + -
440B VAL* 3.8 15.7 - - + -
444B LEU* 3.7 37.9 - - + -
521B LYS* 2.9 45.1 + - + +
524B ALA* 1.3 79.0 - - - +
526B TYR* 1.3 79.3 + - + +
527B TRP 3.5 0.2 - - - -
528B PRO* 3.4 3.6 - - - +
529B ALA* 3.3 22.5 + - - +
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Residues in contact with TYR 526 (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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409B LEU* 3.4 31.9 - - + -
444B LEU* 6.1 0.7 - - + -
447B LEU* 3.6 33.2 - - + +
474B TRP* 3.7 27.3 - + - -
478B LEU* 4.3 1.6 - - + -
521B LYS* 3.5 6.4 + - + -
522B PHE* 3.4 46.0 - + - +
525B ILE* 1.3 87.5 - - + +
527B TRP* 1.3 65.4 + - - +
529B ALA* 3.1 9.7 + - - +
530B PHE* 3.0 42.3 + - + -
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Residues in contact with TRP 527 (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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344B LEU* 4.8 8.3 - - + -
478B LEU* 3.6 45.1 - - + +
479B THR* 4.1 10.5 - - - -
481B TYR* 3.9 21.5 - + + -
482B LEU* 4.3 13.9 - - + -
508B PHE* 3.8 25.4 - + - -
513B HIS* 3.1 32.3 + + - -
522B PHE 2.9 20.2 + - - +
523B HIS* 3.5 19.3 - + - +
526B TYR* 1.3 71.7 - - - +
528B PRO* 1.3 68.6 - - + +
530B PHE* 3.1 18.8 + + + +
531B LEU* 3.1 53.4 + - + +
539B PRO* 4.3 7.2 - - + +
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Residues in contact with PRO 528 (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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416B LEU* 3.6 11.9 - - + -
419B TRP* 4.0 19.5 - - + -
523B HIS 3.0 26.5 - - - +
524B ALA 3.1 25.4 - - - +
525B ILE 3.4 9.4 - - - +
527B TRP* 1.3 85.6 - - + +
529B ALA* 1.3 49.9 + - - +
531B LEU* 3.1 13.7 + - + +
532B LEU* 2.8 41.2 + - - +
538B LEU* 4.2 15.9 - - + +
539B PRO* 5.3 1.8 - - + -
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Residues in contact with ALA 529 (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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407B PHE* 3.7 12.5 - - + -
409B LEU* 3.4 32.3 - - + -
412B PHE* 3.6 23.2 - - + -
416B LEU* 4.1 3.8 - - + +
525B ILE 3.3 8.1 + - - +
526B TYR 3.1 10.4 + - - +
528B PRO* 1.3 76.0 - - - +
530B PHE* 1.3 63.9 + - - +
532B LEU* 3.3 8.0 + - - +
533B SER* 3.0 20.8 + - - -
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Residues in contact with PHE 530 (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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344B LEU* 4.7 7.6 - - + +
348B LEU* 3.9 15.9 - - + +
407B PHE* 3.6 48.0 - + + -
447B LEU* 3.9 23.6 - - + -
449B VAL* 4.5 1.3 - - + -
474B TRP* 3.9 23.1 - - + -
475B LEU* 3.7 30.3 - - + -
478B LEU* 4.1 13.0 - - + -
479B THR* 6.0 0.4 - - - -
526B TYR* 3.0 24.1 + - + -
527B TRP* 3.1 23.5 + + + +
529B ALA* 1.3 75.3 - - - +
531B LEU* 1.3 60.3 + - + +
533B SER* 3.3 4.3 + - - -
534B ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 531 (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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344B LEU* 5.6 2.5 - - + -
482B LEU* 5.5 0.4 - - + -
508B PHE* 3.9 11.0 - - + -
527B TRP* 3.1 60.9 + - + +
528B PRO* 3.1 8.6 + - + +
530B PHE* 1.3 77.5 - - + +
532B LEU* 1.3 57.6 + - - +
534B ALA* 3.4 1.8 + - - -
535B GLY* 3.0 7.3 + - - -
536B LEU* 2.8 62.0 + - + +
537B PRO 3.6 15.0 - - - +
538B LEU* 3.7 12.1 - - + -
539B PRO* 3.8 20.2 - - + -
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Residues in contact with LEU 532 (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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351B LYS* 4.6 4.2 + - - -
412B PHE* 3.9 19.1 - - + -
415B ARG* 3.9 43.6 + - + +
416B LEU* 4.4 15.9 - - + +
419B TRP* 5.8 1.3 - - + -
528B PRO 2.8 27.7 + - - +
529B ALA* 3.5 6.3 - - - +
531B LEU* 1.3 70.8 - - - +
533B SER* 1.3 66.7 + - - +
535B GLY* 3.1 13.0 + - - -
536B LEU 5.0 0.7 - - - +
538B LEU* 4.0 27.6 - - + -
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Residues in contact with SER 533 (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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348B LEU* 3.4 24.1 - - - +
351B LYS* 3.2 32.0 + - - +
353B ASP* 2.6 36.3 + - - +
407B PHE* 4.0 5.2 - - - -
412B PHE* 3.7 12.0 - - - -
415B ARG* 5.4 1.1 - - - +
529B ALA 3.0 12.5 + - - -
530B PHE 3.3 8.7 + - - -
532B LEU* 1.3 75.8 - - - +
534B ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 534 (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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344B LEU* 3.7 26.0 - - + -
347B LYS* 3.6 37.8 + - + +
348B LEU* 4.0 3.8 - - + +
351B LYS* 4.8 1.3 - - - -
530B PHE 3.0 16.4 + - - +
531B LEU 3.9 1.8 - - - +
532B LEU 3.2 0.2 - - - -
533B SER* 1.3 76.6 - - - +
535B GLY* 1.3 60.4 + - - +
536B LEU* 3.6 20.9 + - + +
802B GOL 5.1 2.9 + - - +
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Residues in contact with GLY 535 (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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351B LYS* 5.0 6.1 - - - -
502B PHE* 5.9 0.3 - - - -
531B LEU 3.0 5.0 + - - -
532B LEU* 3.1 12.3 + - - -
533B SER 3.2 1.2 + - - -
534B ALA* 1.3 78.3 - - - +
536B LEU* 1.3 63.1 + - - +
537B PRO* 4.2 2.1 - - - +
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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