Contacts of the helix formed by residues 558 - 570 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A LYS* 4.4 2.4 - - - +
557A SER* 1.3 75.7 - - - +
559A THR* 1.3 67.3 + - - +
560A PRO* 3.2 4.3 - - - -
561A GLU* 3.0 21.0 + - - +
562A THR* 2.9 14.5 + - - +
660A ASP* 3.4 28.4 + - - +
661A LEU 4.4 0.7 + - - -
662A ARG* 3.4 44.6 + - - -
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Residues in contact with THR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A THR 4.6 0.5 + - - -
431A LEU* 3.1 45.1 + - + +
555A ILE* 5.1 1.1 - - + -
556A LYS* 2.9 38.2 + - - +
558A SER* 1.3 77.8 + - - +
560A PRO* 1.3 64.6 - - - +
562A THR* 3.3 9.0 - - + +
563A ILE* 3.0 33.9 + - + +
591A LEU* 3.7 16.8 - - + -
661A LEU* 5.0 7.8 - - + +
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Residues in contact with PRO 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A ILE* 4.0 17.3 - - + -
556A LYS 3.0 14.6 - - - +
557A SER 3.4 12.6 - - - +
558A SER 3.2 2.5 - - - +
559A THR* 1.3 93.1 - - - +
561A GLU* 1.3 66.6 + - + +
563A ILE* 3.9 3.6 + - - +
564A LEU* 3.3 25.2 + - - +
590A THR 5.9 1.8 - - - +
591A LEU* 4.0 19.2 - - + +
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Residues in contact with GLU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A SER* 3.0 12.6 + - - +
560A PRO* 1.3 81.7 - - + +
562A THR* 1.3 66.5 + - - +
564A LEU* 3.0 25.2 + - + +
565A GLU* 3.0 21.4 + - + +
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Residues in contact with THR 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A SER* 2.9 31.6 - - - +
559A THR* 3.3 11.7 + - - -
561A GLU* 1.3 73.3 - - - +
563A ILE* 1.3 69.8 + - - +
565A GLU* 2.9 23.7 + - - +
566A LEU* 3.0 23.8 + - - +
661A LEU* 2.9 27.4 - - + +
662A ARG* 3.1 30.5 - - - +
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Residues in contact with ILE 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LEU* 6.0 0.7 - - + -
425A VAL* 5.6 2.2 - - + -
431A LEU* 4.0 23.3 - - + -
559A THR* 3.0 26.4 + - + +
560A PRO 4.0 4.9 - - - +
562A THR* 1.3 86.7 + - - +
564A LEU* 1.3 55.6 + - - +
566A LEU* 3.3 9.9 + - + +
567A GLN* 2.7 47.9 + - + +
573A ILE* 4.3 21.3 - - + +
591A LEU* 3.6 29.6 - - + +
592A GLY* 5.2 0.4 - - - -
593A ILE* 4.3 18.4 - - + -
661A LEU* 5.0 6.7 - - + -
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A PRO 3.3 19.5 - - - +
561A GLU* 3.0 16.2 + - + +
563A ILE* 1.3 78.0 - - - +
565A GLU* 1.3 62.4 + - - +
567A GLN* 3.0 24.8 + - + +
568A GLN* 3.0 27.7 + - + +
591A LEU 4.3 14.6 - - - +
592A GLY* 5.8 1.1 - - - -
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Residues in contact with GLU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A GLU* 3.0 20.2 + - + +
562A THR* 2.9 19.1 + - - +
564A LEU* 1.3 77.2 - - + +
566A LEU* 1.3 63.5 + - + +
567A GLN 3.3 0.2 + - - -
568A GLN* 3.3 8.0 + - - +
569A SER* 3.0 26.6 + - - -
662A ARG 5.1 5.4 - - - +
663A GLY 5.9 0.2 + - - -
665A ALA* 3.8 21.2 - - + +
669A ARG* 3.9 11.4 + - - -
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Residues in contact with LEU 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LEU* 3.5 31.6 - - + -
562A THR* 3.0 25.9 + - - +
563A ILE* 3.8 10.1 - - + +
565A GLU* 1.3 79.6 - - + +
567A GLN* 1.3 61.7 + - - +
569A SER* 3.6 8.6 - - - -
570A GLY 3.2 2.6 + - - -
571A ILE* 2.8 58.2 + - + +
573A ILE* 4.1 11.9 - - + -
661A LEU* 5.1 1.3 - - + -
664A ILE* 3.9 27.4 - - + -
665A ALA* 4.2 14.4 - - + -
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Residues in contact with GLN 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ILE* 2.7 39.0 + - + +
564A LEU* 3.1 19.2 - - + +
566A LEU* 1.3 76.3 - - - +
568A GLN* 1.3 68.8 + - + +
570A GLY* 3.3 12.6 + - - -
571A ILE 3.9 5.6 - - - +
572A GLU* 5.1 0.9 - - - -
573A ILE* 3.5 23.8 + - - +
591A LEU 5.1 0.6 + - - -
592A GLY* 3.8 27.1 + - - -
593A ILE* 6.3 0.2 - - - -
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Residues in contact with GLN 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A LEU* 3.0 22.8 + - + +
565A GLU* 3.7 7.4 - - - +
567A GLN* 1.3 75.2 - - - +
569A SER* 1.3 67.7 + - - +
570A GLY* 3.3 1.6 + - - -
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Residues in contact with SER 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A GLU 3.0 17.6 + - - -
566A LEU* 3.6 12.6 - - - -
568A GLN* 1.3 78.4 - - - +
570A GLY* 1.3 57.1 + - - +
571A ILE* 3.6 11.9 - - - +
668A ARG* 3.2 42.9 + - - +
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Residues in contact with GLY 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A VAL 5.5 0.4 - - - -
421A ASN* 3.3 12.0 - - - +
566A LEU 3.2 1.8 + - - -
567A GLN 3.3 8.2 + - - -
568A GLN 3.2 4.1 - - - -
569A SER* 1.3 80.0 - - - +
571A ILE* 1.3 62.6 + - - +
572A GLU* 3.0 20.1 - - - +
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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