Contacts of the helix formed by residues 559 - 572 (chain A) in PDB entry 1SL0
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 THR 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A ALA* 4.8 7.0 - - - -
555A PHE* 3.3 27.9 + - - +
556A LEU* 4.1 4.3 - - - -
557A GLU 4.5 1.8 - - - -
558A ASN* 1.3 80.4 - - - +
560A PRO* 1.3 65.4 - - - +
561A ALA* 3.1 6.9 + - - +
562A ILE* 3.4 32.5 + - - +
563A ALA* 3.7 6.9 + - - +
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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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556A LEU 5.1 1.6 - - - +
557A GLU* 4.3 9.1 - - - +
558A ASN 3.6 7.0 - - - +
559A THR* 1.3 87.6 - - - +
561A ALA* 1.3 56.2 + - + +
563A ALA* 3.0 14.2 - - + +
564A ALA* 2.5 35.4 + - - +
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Residues in contact with ALA 561 (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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488A MET* 3.4 38.6 - - - +
491A PHE* 4.4 2.9 - - - -
492A ASP* 4.1 17.5 - - + +
559A THR* 3.1 1.3 - - - -
560A PRO* 1.3 79.8 - - + +
562A ILE* 1.3 63.9 + - + +
563A ALA 3.0 1.3 - - - -
564A ALA* 2.9 10.5 + - - +
565A LEU* 2.8 28.9 + - - +
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Residues in contact with ILE 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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484A LEU* 4.3 18.8 - - + -
488A MET* 3.7 29.4 - - + -
528A PHE* 4.4 24.7 - - + -
555A PHE* 4.5 17.3 - - + -
556A LEU* 5.8 4.5 - - + -
559A THR* 3.4 33.7 - - - +
561A ALA* 1.3 76.5 - - + +
563A ALA* 1.3 57.8 + - - +
565A LEU* 3.6 6.3 - - - +
566A ARG* 3.0 40.6 + - + +
610A LEU* 4.3 19.7 - - + -
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Residues in contact with ALA 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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556A LEU* 4.0 24.1 - - + +
559A THR 3.7 1.9 + - - +
560A PRO* 3.0 24.8 - - + +
562A ILE* 1.3 80.0 - - - +
564A ALA* 1.3 62.0 + - - +
566A ARG* 3.7 9.7 - - - +
567A GLU* 3.2 23.2 + - - +
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Residues in contact with ALA 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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491A PHE* 3.5 37.2 - - + -
560A PRO 2.5 16.5 + - - +
561A ALA* 3.0 11.0 - - - +
563A ALA* 1.3 72.0 - - - +
565A LEU* 1.3 69.5 + - - +
567A GLU* 3.2 6.7 + - - +
568A SER* 2.9 20.6 + - - -
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Residues in contact with LEU 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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484A LEU* 3.5 24.0 - - + -
487A PHE* 2.8 38.6 - - + +
488A MET* 3.1 35.0 - - + +
490A ARG* 6.0 0.7 - - - +
491A PHE* 3.3 20.9 - - + -
561A ALA 2.8 10.2 + - - +
562A ILE* 3.6 8.7 - - - +
564A ALA* 1.3 71.6 - - - +
566A ARG* 1.3 66.5 + - - +
568A SER* 2.9 17.1 + - - -
569A ILE* 3.1 18.2 + - + +
610A LEU* 4.1 20.0 - - + -
613A LEU* 5.3 2.9 - - + -
614A LEU* 5.3 0.4 - - + -
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Residues in contact with ARG 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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528A PHE* 5.5 9.0 - - - -
556A LEU* 5.8 6.5 - - - -
562A ILE* 3.0 31.2 + - - +
563A ALA* 3.7 9.0 - - - +
565A LEU* 1.3 78.6 - - - +
567A GLU* 1.3 60.9 + - - +
569A ILE* 3.5 6.7 + - - +
570A GLN* 3.3 22.2 + - - +
606A PRO 5.4 5.7 + - - -
607A HIS* 4.6 28.6 + - - +
609A ALA* 6.2 0.2 - - - +
610A LEU* 4.0 36.3 - - + +
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Residues in contact with GLU 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 ALA 3.2 14.4 + - - +
564A ALA* 3.2 6.2 + - - +
565A LEU 3.1 0.8 - - - -
566A ARG* 1.3 76.5 - - - +
568A SER* 1.3 65.0 + - - +
569A ILE 3.1 0.3 + - - -
570A GLN* 3.3 7.1 + - - +
571A GLN* 3.0 22.9 + - - +
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Residues in contact with SER 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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490A ARG* 5.8 4.9 - - - -
491A PHE* 3.8 23.6 - - - -
564A ALA 2.9 12.0 + - - -
565A LEU* 2.9 9.9 + - - -
567A GLU* 1.3 76.4 - - - +
569A ILE* 1.3 61.2 + - - +
571A GLN* 3.2 13.5 - - - +
572A THR* 3.1 20.8 + - - -
195C GLU* 4.7 13.8 - - - +
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Residues in contact with ILE 569 (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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565A LEU* 3.1 12.0 + - + +
566A ARG* 3.8 7.2 - - - +
568A SER* 1.3 74.7 - - - +
570A GLN* 1.3 60.7 + - - +
571A GLN 2.8 1.8 - - - -
572A THR* 2.5 38.4 + - - +
573A LEU* 3.6 5.8 + - + +
593A ILE* 4.7 22.2 - - + -
609A ALA* 3.8 25.4 - - + -
610A LEU* 3.7 26.9 - - + +
613A LEU* 3.3 38.1 - - + -
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Residues in contact with GLN 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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566A ARG 3.3 11.5 + - - +
567A GLU* 3.7 9.9 - - - +
569A ILE* 1.3 78.9 - - - +
571A GLN* 1.3 56.9 + - - +
573A LEU* 5.1 0.7 - - - -
574A VAL* 2.8 54.3 + - + +
606A PRO* 6.4 0.7 - - + -
609A ALA* 5.8 1.5 - - - +
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Residues in contact with GLN 571 (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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567A GLU 3.0 13.1 + - - +
568A SER* 3.2 18.4 - - - +
569A ILE 2.8 0.4 + - - -
570A GLN* 1.3 78.5 - - - +
572A THR* 1.3 57.8 + - - +
573A LEU 3.5 2.5 + - - -
574A VAL 3.9 9.9 - - - +
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Residues in contact with THR 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A SER 3.1 13.9 + - - -
569A ILE* 2.5 18.0 + - - +
571A GLN* 1.3 73.1 - - - +
573A LEU* 1.3 65.0 + - - +
589A LYS* 5.5 0.9 - - - -
590A ARG* 4.6 10.8 - - + +
592A TRP 4.8 1.4 - - - +
593A ILE* 4.6 16.4 - - + +
195C GLU* 4.5 28.2 + - + +
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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