Contacts of the helix formed by residues 559 - 568 (chain A) in PDB entry 4I5L
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 GLU 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A THR* 5.3 2.8 - - - +
522A LEU* 4.0 8.5 - - - +
526A LEU* 3.9 22.9 - - + +
555A THR* 2.9 30.8 + - + +
558A SER* 1.3 91.9 - - - +
560A VAL* 1.3 65.4 + - + +
562A PRO* 3.4 8.8 - - - +
563A ILE* 3.5 20.1 - - - +
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Residues in contact with VAL 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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522A LEU* 4.2 18.8 - - + -
526A LEU* 4.5 5.6 - - + -
544A LEU* 4.0 23.1 - - + +
551A LEU* 3.7 28.9 - - + -
555A THR 3.2 10.7 + - - +
556A LEU* 3.5 23.6 - - + +
559A GLU* 1.3 74.7 - - - +
561A LYS* 1.3 67.3 + - - +
563A ILE* 3.1 6.2 + - - +
564A LEU* 3.1 40.9 + - + +
586A LEU* 4.6 2.2 - - + -
588A LEU* 4.6 2.7 - - + -
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Residues in contact with LYS 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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556A LEU 2.8 20.9 + - - +
557A GLN* 3.6 29.1 + - - +
560A VAL* 1.3 73.1 - - - +
562A PRO* 1.4 65.9 - - + +
564A LEU* 3.2 1.7 + - - +
565A GLU* 2.9 49.4 + - + +
583A LEU* 4.1 10.3 - - + -
588A LEU* 3.2 49.5 + - + +
589A ALA 5.7 0.6 + - - -
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Residues in contact with PRO 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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557A GLN 3.7 9.4 - - - +
558A SER* 3.5 16.6 - - - +
559A GLU 3.4 17.9 - - - +
561A LYS* 1.4 96.5 - - + +
563A ILE* 1.3 58.1 + - + +
565A GLU* 3.4 9.3 + - + +
566A LYS* 3.1 29.2 + - - +
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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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526A LEU* 3.9 41.3 - - + +
529A ALA* 3.6 28.3 - - + -
544A LEU* 4.3 11.4 - - + -
559A GLU 3.5 15.0 - - - +
560A VAL 3.1 7.0 + - - +
562A PRO* 1.3 76.3 - - + +
564A LEU* 1.3 61.1 + - - +
566A LYS* 3.2 23.0 + - + +
567A LEU* 2.9 35.1 + - + +
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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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541A ALA* 3.9 19.3 - - + -
544A LEU* 3.8 22.2 - - + -
560A VAL* 3.1 33.8 + - + +
561A LYS 3.7 2.5 - - - +
563A ILE* 1.3 74.6 - - - +
565A GLU* 1.3 56.7 + - - +
567A LEU* 3.0 9.2 + - + +
568A THR* 2.9 33.2 + - - +
579A ALA* 3.6 7.1 - - + +
582A ALA* 3.6 33.4 - - + -
583A LEU* 3.7 31.6 - - + +
586A LEU* 4.3 9.9 - - + -
588A LEU* 4.3 4.0 - - + -
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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 LYS* 2.9 43.6 + - + +
562A PRO* 3.6 8.3 - - + +
564A LEU* 1.3 74.9 - - - +
566A LYS* 1.3 63.5 + - - +
568A THR* 2.5 32.2 + - - -
569A GLN* 3.2 17.4 + - - +
583A LEU* 3.4 26.6 - - - +
588A LEU 4.4 3.1 - - - +
589A ALA* 5.4 1.7 - - - -
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Residues in contact with LYS 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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529A ALA* 6.3 2.5 - - + -
562A PRO 3.1 14.7 + - - +
563A ILE* 3.2 25.6 + - + +
565A GLU* 1.3 74.8 - - - +
567A LEU* 1.3 61.9 + - + +
569A GLN* 3.0 37.6 + - + +
570A ASP* 3.7 4.0 + - - -
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Residues in contact with LEU 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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529A ALA* 3.7 33.0 - - + +
537A ARG* 4.0 26.0 - - + +
540A VAL* 4.0 20.6 - - + -
541A ALA* 4.2 13.7 - - + +
563A ILE* 2.9 21.9 + - + +
564A LEU* 3.0 14.5 + - + +
566A LYS* 1.3 81.0 - - + +
568A THR* 1.3 61.3 + - - +
569A GLN 3.0 1.7 + - - -
570A ASP* 3.2 23.7 + - - +
575A VAL* 3.5 26.4 - - + +
576A LYS* 3.9 1.2 - - - -
579A ALA* 3.6 12.3 - - + -
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Residues in contact with THR 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 2.9 18.1 + - - +
565A GLU* 2.5 27.0 + - - +
567A LEU* 1.3 75.3 - - - +
569A GLN* 1.3 59.3 + - - +
570A ASP 3.5 1.1 - - - -
576A LYS* 3.5 29.1 + - - +
579A ALA* 3.7 14.6 - - + -
580A GLN* 4.0 20.0 - - + +
583A LEU* 3.7 25.1 - - + -
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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