Contacts of the helix formed by residues 558 - 570 (chain B) in PDB entry 3RFU
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 SER 558 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556B LYS* 4.4 1.9 - - - +
557B SER* 1.3 74.4 - - - +
559B THR* 1.3 67.4 + - - +
560B PRO* 3.2 4.7 - - - +
561B GLU* 3.0 21.2 + - - +
562B THR* 2.9 13.7 + - - +
660B ASP* 3.4 29.2 + - - +
661B LEU 4.4 0.5 + - - -
662B ARG* 3.4 44.9 + - - -
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Residues in contact with THR 559 (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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430B THR 4.6 0.3 + - - -
431B LEU* 3.1 45.1 + - + +
555B ILE* 5.1 0.9 - - - -
556B LYS* 2.9 38.6 + - - +
558B SER* 1.3 79.1 + - - +
560B PRO* 1.3 63.7 - - - +
562B THR* 3.3 9.6 - - + +
563B ILE* 3.0 34.2 + - + +
591B LEU* 3.7 17.0 - - + -
661B LEU* 5.0 7.1 - - + +
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Residues in contact with PRO 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ILE* 4.0 18.4 - - + -
556B LYS 3.0 14.8 - - - +
557B SER 3.4 12.1 - - - +
558B SER 3.2 2.5 - - - +
559B THR* 1.3 93.5 - - - +
561B GLU* 1.3 67.9 + - + +
563B ILE* 4.0 3.1 - - - +
564B LEU* 3.3 24.9 + - - +
590B THR 5.9 2.0 - - - +
591B LEU* 4.0 19.3 - - + +
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Residues in contact with GLU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B SER* 3.0 12.6 + - - +
560B PRO* 1.3 82.0 - - + +
562B THR* 1.3 65.3 + - - +
564B LEU* 3.0 24.9 + - + +
565B GLU* 3.0 21.5 + - + +
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Residues in contact with THR 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B SER* 2.9 32.1 - - - +
559B THR* 3.3 11.7 + - - +
561B GLU* 1.3 74.0 - - - +
563B ILE* 1.3 68.8 + - - +
565B GLU* 2.8 22.9 + - - +
566B LEU* 3.0 25.0 + - - +
661B LEU* 2.9 29.2 - - + +
662B ARG* 3.1 30.3 - - - +
665B ALA* 6.5 0.2 - - - -
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Residues in contact with ILE 563 (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 LEU* 6.0 0.4 - - + -
425B VAL* 5.6 2.7 - - + -
431B LEU* 4.0 22.9 - - + -
559B THR* 3.0 26.6 + - + +
560B PRO 4.0 4.7 - - - +
562B THR* 1.3 84.4 + - - +
564B LEU* 1.3 57.3 + - - +
566B LEU* 3.3 10.9 + - + +
567B GLN* 2.7 46.3 + - + +
573B ILE* 4.3 20.0 - - + -
591B LEU* 3.6 29.8 - - + +
593B ILE* 4.3 19.7 - - + +
661B LEU* 5.0 6.5 - - + -
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Residues in contact with LEU 564 (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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560B PRO 3.3 19.1 - - - +
561B GLU* 3.0 16.7 + - + +
563B ILE* 1.3 77.0 - - - +
565B GLU* 1.3 63.5 + - - +
567B GLN* 3.0 24.4 + - + +
568B GLN* 3.0 26.8 + - - +
591B LEU 4.3 14.8 - - - +
592B GLY* 5.8 1.1 - - - -
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Residues in contact with GLU 565 (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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561B GLU* 3.0 20.6 + - + +
562B THR* 2.8 18.7 + - - +
564B LEU* 1.3 77.0 - - + +
566B LEU* 1.3 63.1 + - + +
568B GLN* 3.3 8.2 + - - +
569B SER* 3.0 27.4 + - - -
662B ARG 5.1 4.9 - - - +
663B GLY 5.9 0.3 + - - -
665B ALA* 3.8 21.1 - - + +
669B ARG* 3.9 10.6 + - - -
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Residues in contact with LEU 566 (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 LEU* 3.5 32.1 - - + -
562B THR* 3.0 25.9 + - - +
563B ILE* 3.8 9.6 - - + +
565B GLU* 1.3 80.4 - - + +
567B GLN* 1.3 60.4 + - - +
569B SER* 3.8 7.4 - - - -
570B GLY 3.2 2.4 + - - -
571B ILE* 2.9 58.8 + - + +
573B ILE* 4.1 12.1 - - + -
661B LEU* 5.1 1.3 - - + -
664B ILE* 3.9 26.9 - - + -
665B ALA* 4.2 15.5 - - + -
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Residues in contact with GLN 567 (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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563B ILE* 2.7 40.1 + - + +
564B LEU* 3.1 19.4 - - + +
566B LEU* 1.3 77.0 - - - +
568B GLN* 1.3 68.2 + - + +
570B GLY* 3.3 12.8 + - - -
571B ILE 3.9 6.1 + - - +
572B GLU* 5.1 0.9 - - - -
573B ILE* 3.5 24.1 + - - +
591B LEU 5.1 0.4 + - - -
592B GLY* 3.8 27.1 + - - -
593B ILE* 5.6 0.4 - - - +
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Residues in contact with GLN 568 (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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564B LEU* 3.0 22.0 + - + +
565B GLU* 3.7 7.0 - - - +
567B GLN* 1.3 74.9 - - - +
569B SER* 1.3 67.7 + - - +
570B GLY* 3.3 1.0 + - - -
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Residues in contact with SER 569 (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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565B GLU 3.0 17.6 + - - -
566B LEU* 3.6 12.6 - - - -
568B GLN* 1.3 79.1 - - - +
570B GLY* 1.3 57.1 + - - +
571B ILE* 3.6 11.1 - - - +
668B ARG* 3.2 42.7 + - - +
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Residues in contact with GLY 570 (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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420B VAL 5.5 0.4 - - - -
421B ASN* 3.3 11.8 - - - +
566B LEU 3.2 1.8 + - - -
567B GLN 3.3 7.8 + - - -
568B GLN 3.2 4.3 - - - -
569B SER* 1.3 79.3 - - - +
571B ILE* 1.3 62.4 + - - +
572B GLU* 3.0 20.3 - - - +
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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