Contacts of the helix formed by residues 588 - 596 (chain A) in PDB entry 5IYB
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 GLY 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A PHE* 3.5 47.2 - - - -
549A THR* 4.7 0.9 - - - -
550A LYS 5.0 3.6 + - - -
551A ARG* 5.9 1.0 - - - +
553A VAL* 3.3 18.4 + - - +
555A LEU* 5.0 1.6 - - - -
587A THR* 1.3 74.5 - - - +
589A LYS* 1.3 63.0 + - - +
591A ILE 3.4 0.7 + - - -
592A PHE* 3.2 17.7 + - - +
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Residues in contact with LYS 589 (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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549A THR* 2.8 33.3 + - - +
551A ARG* 3.6 28.1 - - - +
587A THR* 3.4 1.0 - - - -
588A GLY* 1.3 76.3 - - - +
590A GLN* 1.3 57.2 + - - +
592A PHE* 3.3 4.8 + - - +
593A SER* 2.9 31.1 + - - -
635A LEU* 4.0 31.7 - - + +
636A ILE 4.2 2.2 - - - +
637A MET* 4.1 14.6 - - - +
638A GLY* 3.7 32.9 + - - +
639A ILE* 4.1 3.6 - - - +
119H GLY 3.4 11.0 - - - +
120H GLY* 3.5 31.9 - - - -
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Residues in contact with GLN 590 (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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575A PRO* 4.8 12.9 - - + +
576A GLN 2.8 28.7 + - - +
578A ALA* 3.3 20.8 + - - +
586A TRP* 3.6 17.4 - - + -
587A THR* 3.3 35.3 + - - +
588A GLY 3.3 0.2 - - - -
589A LYS* 1.3 78.3 - - - +
591A ILE* 1.3 64.8 + - + +
593A SER* 3.0 23.0 + - - -
594A LEU* 3.6 7.3 + - - +
635A LEU 5.6 0.4 - - - -
93H TYR* 4.9 6.9 + - - -
119H GLY* 4.2 9.4 + - - -
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Residues in contact with ILE 591 (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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548A PHE* 4.4 11.4 - - + -
555A LEU* 5.1 6.1 - - + -
560A VAL* 3.8 23.3 - - + -
563A LEU* 4.4 27.1 - - + -
564A LEU* 5.2 6.5 - - + -
567A LEU* 5.5 1.1 - - + +
575A PRO* 4.5 10.1 - - + -
586A TRP* 3.6 35.9 - - + -
587A THR 3.4 12.7 + - - +
588A GLY 4.1 5.2 - - - +
590A GLN* 1.3 75.7 - - - +
592A PHE* 1.3 61.7 + - - +
594A LEU* 3.1 29.1 + - + +
595A ILE* 3.8 7.7 + - + +
675A VAL* 6.0 4.9 - - + -
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Residues in contact with PHE 592 (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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545A VAL* 4.0 5.6 - - + -
548A PHE* 4.4 7.3 - + + -
549A THR* 4.4 13.5 - - + -
588A GLY 3.2 12.1 + - - +
589A LYS* 3.4 11.7 - - - +
590A GLN 3.2 0.2 - - - -
591A ILE* 1.3 76.5 - - - +
593A SER* 1.3 66.0 + - - +
595A ILE* 2.9 53.5 + - + +
596A ILE* 3.6 18.2 + - + -
635A LEU* 3.9 22.2 - - + -
640A LEU* 3.3 30.1 - - + -
652A LEU* 4.1 14.1 - - + -
672A ILE* 3.9 21.8 - - + -
675A VAL* 5.8 1.1 - - + -
676A ILE* 4.5 15.0 - - + -
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Residues in contact with SER 593 (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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589A LYS 2.9 16.5 + - - -
590A GLN* 3.0 13.7 + - - -
592A PHE* 1.3 75.2 - - - +
594A LEU* 1.3 63.3 + - - +
596A ILE* 3.5 23.6 - - - +
633A GLY 3.6 9.4 - - - +
634A GLU* 3.3 25.1 - - - +
635A LEU* 2.6 29.4 + - - +
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Residues in contact with LEU 594 (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* 3.6 29.8 - - + -
567A LEU* 4.0 19.6 - - + +
569A THR* 5.6 1.4 + - - -
570A TRP* 4.4 11.9 - - + +
571A ASP* 5.3 4.3 - - - +
573A LYS 5.6 0.4 - - - +
575A PRO* 3.7 36.8 - - + -
590A GLN 4.3 6.1 - - - +
591A ILE* 3.1 18.6 + - + +
592A PHE 3.0 1.2 + - - -
593A SER* 1.3 82.7 - - - +
595A ILE* 1.3 61.4 + - - +
596A ILE 3.3 7.1 + - - +
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Residues in contact with ILE 595 (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 LEU* 4.1 19.5 - - + -
591A ILE* 4.5 8.3 - - + +
592A PHE* 2.9 59.4 + - + +
594A LEU* 1.3 76.7 - - - +
596A ILE* 1.3 63.7 + - + +
597A PRO* 4.2 1.0 - - - +
668A PHE* 3.4 38.1 - - + +
671A ASN* 4.3 6.9 - - + +
672A ILE* 4.1 12.3 - - + +
675A VAL* 3.4 44.6 - - + -
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Residues in contact with ILE 596 (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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592A PHE* 4.0 22.9 - - + +
593A SER* 3.5 21.8 - - - +
594A LEU 3.3 6.5 - - - +
595A ILE* 1.3 94.5 - - + +
597A PRO* 1.4 63.7 - - + +
598A GLY* 3.1 10.6 + - - -
600A ILE* 3.7 27.1 - - + -
630A VAL* 4.1 14.1 - - + -
633A GLY 4.0 20.0 - - - +
634A GLU* 4.3 1.8 - - - +
635A LEU* 4.3 11.4 - - - +
652A LEU* 4.5 4.5 - - + -
668A PHE* 3.7 21.3 - - + -
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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