Contacts of the helix formed by residues 570 - 580 (chain B) in PDB entry 4F1P
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 HIS 570 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524B PRO* 5.9 0.2 - - - -
569B LEU* 1.3 107.5 + - + +
571B PRO* 1.4 67.5 - - - +
572B GLY 3.3 2.2 - - - -
573B ALA* 3.3 12.4 + - + +
574B LEU* 3.0 23.2 + - - +
577B ARG* 5.6 2.1 + - - +
802B SO4 3.1 29.7 + - - +
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Residues in contact with PRO 571 (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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524B PRO* 4.8 10.3 - - + -
569B LEU* 3.7 8.0 - - - +
570B HIS* 1.4 85.8 - - - +
572B GLY* 1.3 56.3 + - - +
574B LEU* 3.3 7.5 + - + +
575B LEU 2.9 24.8 + - - -
591B ALA* 3.5 10.7 - - + +
594B HIS* 3.5 26.0 - - + +
595B GLY 4.3 1.6 - - - -
596B ALA* 3.4 32.2 - - - +
802B SO4 3.2 15.3 - - - +
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Residues in contact with GLY 572 (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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571B PRO* 1.3 73.2 - - - +
573B ALA* 1.3 55.5 + - - +
575B LEU* 3.5 4.8 + - - +
576B PHE* 3.0 20.1 + - - +
596B ALA* 3.9 14.4 - - - +
597B ASP 4.5 0.9 - - - -
600B TRP* 3.5 38.5 - - - +
802B SO4 2.7 21.9 + - - -
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Residues in contact with ALA 573 (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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570B HIS* 3.3 15.7 + - + +
572B GLY* 1.3 74.1 - - - +
574B LEU* 1.3 59.6 + - - +
576B PHE* 3.2 2.4 + - - +
577B ARG* 2.9 41.1 + - - +
600B TRP* 3.8 29.1 - - + -
802B SO4 3.2 10.5 + - - +
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Residues in contact with LEU 574 (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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524B PRO* 3.5 43.5 - - + +
570B HIS 3.0 14.9 + - - +
571B PRO* 3.3 8.5 + - + +
573B ALA* 1.3 73.2 - - - +
575B LEU* 1.3 60.4 + - - +
577B ARG* 3.2 35.9 + - + +
578B ALA* 2.8 32.8 + - + +
587B THR* 3.8 28.7 - - + +
591B ALA* 4.3 7.6 - - + -
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Residues in contact with LEU 575 (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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571B PRO 2.9 16.7 + - - +
572B GLY 3.6 4.5 - - - +
574B LEU* 1.3 74.7 - - - +
576B PHE* 1.3 59.3 + - - +
578B ALA* 3.9 3.3 - - - -
579B SER* 2.7 34.2 + - - -
588B MET* 3.7 42.6 - - + +
591B ALA* 3.7 9.0 - - + +
592B LEU* 4.0 13.5 - - + -
596B ALA* 3.9 10.5 - - + -
597B ASP 3.5 25.1 - - - +
598B VAL* 3.8 12.6 - - - -
610B PRO* 3.8 18.6 - - + -
626B LEU* 4.0 14.1 - - + -
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Residues in contact with PHE 576 (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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572B GLY 3.0 15.5 + - - +
573B ALA 3.2 8.7 + - - +
575B LEU* 1.3 77.8 - - - +
577B ARG* 1.3 68.7 + - + +
579B SER* 3.4 3.5 + - - -
600B TRP* 3.6 24.5 - + + -
602B ASN* 3.8 26.5 - - + -
606B ASP* 4.8 1.6 - - - -
608B ALA* 3.3 37.0 - - + -
609B THR 3.6 24.7 - - - -
610B PRO* 3.9 10.0 - - + +
613B GLN* 3.2 57.9 + - - +
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Residues in contact with ARG 577 (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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570B HIS* 5.6 2.4 + - - +
573B ALA* 2.9 21.2 + - - +
574B LEU* 3.6 42.1 - - + +
576B PHE* 1.3 81.9 - - + +
578B ALA* 1.3 58.3 + - - +
580B GLY* 3.1 22.3 + - - +
582B PRO 5.6 0.2 - - - +
613B GLN* 4.7 4.3 + - - +
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Residues in contact with ALA 578 (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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574B LEU* 2.8 22.2 + - + +
575B LEU 4.1 0.9 - - - +
577B ARG* 1.3 72.5 - - - +
579B SER* 1.3 57.7 + - - +
580B GLY 3.3 0.7 - - - -
582B PRO 5.7 0.9 - - - -
583B PRO* 3.2 8.0 - - - +
584B SER* 2.9 33.4 + - - +
587B THR* 3.7 33.4 - - + -
588B MET* 3.7 19.6 - - + +
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Residues in contact with SER 579 (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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575B LEU* 2.7 22.2 + - - +
576B PHE 3.6 6.3 - - - -
577B ARG 3.1 0.4 - - - -
578B ALA* 1.3 75.0 - - - +
580B GLY* 1.3 64.6 + - - +
583B PRO* 3.8 10.4 - - - +
588B MET* 3.5 29.5 - - - +
610B PRO* 3.5 35.8 - - - +
613B GLN* 3.9 2.5 - - - -
614B ALA* 3.4 22.2 - - - +
617B ALA* 3.9 0.2 - - - +
622B ALA* 4.9 0.4 - - - -
626B LEU* 3.8 1.5 - - - +
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Residues in contact with GLY 580 (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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577B ARG 3.1 14.8 + - - +
578B ALA 3.8 0.7 - - - +
579B SER* 1.3 78.6 - - - +
581B HIS* 1.3 62.8 + - - -
582B PRO 3.0 4.0 - - - +
583B PRO* 2.9 24.8 - - - +
613B GLN* 3.4 32.3 - - - +
617B ALA* 3.9 2.5 - - - -
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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