Contacts of the helix formed by residues 590 - 603 (chain A) in PDB entry 4BL8
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 HIS 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A ASP* 2.9 13.7 + - - +
589A PRO* 1.3 86.4 - - + +
591A LEU* 1.3 60.6 - - - +
592A GLN 3.5 0.7 - - - -
593A GLU* 3.5 43.4 - - - +
594A ARG* 4.1 6.2 + - - +
172B TYR* 5.5 3.0 + - - +
174B ASN* 3.0 56.4 + - + -
175B GLY* 3.4 16.3 + - - +
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Residues in contact with LEU 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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562A LEU* 4.5 25.3 - - + +
565A THR* 4.8 7.9 - - - +
566A VAL* 4.0 20.4 - - + -
584A ILE* 3.5 33.2 - - + +
585A PHE* 4.2 13.2 - - + -
588A ASP* 3.0 37.4 + - + +
590A HIS* 1.3 78.1 - - - +
592A GLN* 1.3 66.8 + - - +
593A GLU 3.0 2.2 - - - -
594A ARG* 2.9 23.9 + - + +
595A VAL* 3.2 13.7 + - - +
172B TYR* 5.5 8.3 - - + +
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Residues in contact with GLN 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A SER* 5.5 0.3 + - - -
553A GLN* 6.0 0.2 + - - -
585A PHE* 3.7 38.9 - - + +
589A PRO 3.3 12.8 + - - +
591A LEU* 1.3 78.7 - - - +
593A GLU* 1.3 62.2 + - + +
595A VAL* 3.3 14.5 + - - +
596A ASP* 3.1 48.9 + - - +
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Residues in contact with GLU 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 PRO 5.1 1.5 - - - +
590A HIS* 3.5 44.9 + - - +
591A LEU 3.0 0.2 - - - -
592A GLN* 1.3 77.7 - - + +
594A ARG* 1.3 64.0 + - - +
595A VAL 3.2 0.2 + - - -
596A ASP* 3.2 9.6 + - - +
597A LYS* 2.9 42.5 + - - +
175B GLY* 5.7 2.3 - - - -
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Residues in contact with ARG 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A TRP* 3.7 26.7 - - + -
561A GLU* 4.3 10.3 + - - -
562A LEU* 4.8 23.4 - - + +
590A HIS 4.1 6.4 + - - +
591A LEU* 2.9 19.5 + - + +
593A GLU* 1.3 78.4 - - - +
595A VAL* 1.3 57.9 + - - +
597A LYS* 3.6 15.4 + - - +
598A GLY* 2.9 34.6 + - - +
92B PRO* 5.6 2.8 + - - +
96B ASP* 3.7 31.8 + - - -
99B ARG* 4.9 7.4 - - - +
172B TYR* 5.7 4.0 - - - +
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A SER* 4.7 13.2 - - - +
553A GLN* 5.7 2.9 - - - +
554A TRP* 4.0 23.7 - - + -
559A ILE* 4.0 11.4 - - + -
562A LEU* 3.9 17.0 - - + -
585A PHE* 3.8 21.8 - - + -
591A LEU 3.2 12.0 + - - +
592A GLN* 3.7 17.0 - - - +
593A GLU 3.1 0.6 - - - -
594A ARG* 1.3 75.8 - - - +
596A ASP* 1.3 67.3 + - - +
598A GLY* 3.0 2.6 + - - -
599A ILE* 2.9 38.3 + - + +
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Residues in contact with ASP 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A GLN* 3.1 38.4 + - - +
593A GLU* 3.2 10.4 + - - +
595A VAL* 1.3 77.1 - - - +
597A LYS* 1.3 58.5 + - + +
599A ILE* 3.1 14.6 + - - +
600A GLU* 3.0 27.0 + - - +
726A ARG* 5.2 5.2 - - - -
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Residues in contact with LYS 597 (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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593A GLU* 2.9 33.5 + - - +
594A ARG* 3.8 17.7 - - - +
596A ASP* 1.3 75.9 - - + +
598A GLY* 1.3 63.2 + - - +
600A GLU* 3.1 21.7 + - - +
601A THR* 3.0 22.8 + - + +
99B ARG* 5.8 9.5 - - - +
102B GLY* 5.3 14.0 - - - +
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Residues in contact with GLY 598 (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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554A TRP* 3.0 29.9 + - - -
594A ARG* 2.9 19.8 + - - +
595A VAL 3.0 4.9 + - - -
597A LYS* 1.3 76.0 - - - +
599A ILE* 1.3 57.4 + - - +
601A THR* 3.9 5.6 - - - -
602A ASP* 2.9 35.6 + - - +
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Residues in contact with ILE 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A GLN* 3.8 23.3 - - + +
554A TRP* 3.8 18.2 - - + -
595A VAL* 2.9 28.6 + - + +
596A ASP* 3.5 14.6 - - - +
597A LYS 3.1 0.4 - - - -
598A GLY* 1.3 75.2 - - - +
600A GLU* 1.3 61.1 + - - +
601A THR 3.1 1.8 - - - -
603A GLY* 2.8 30.3 + - - +
604A SER 4.3 5.8 - - - +
723A LEU* 3.5 30.7 - - + -
726A ARG* 5.1 5.8 - - + -
727A GLY* 3.8 26.2 - - - +
731A HIS* 3.7 2.9 + - - -
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Residues in contact with GLU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ASP 3.0 12.3 + - - +
597A LYS* 3.1 16.3 + - - +
599A ILE* 1.3 78.0 - - - +
601A THR* 1.3 66.0 + - - +
726A ARG* 4.2 33.6 + - + +
730A LEU* 6.3 1.6 - - + -
731A HIS* 3.0 18.2 + - - -
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Residues in contact with THR 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A LYS* 3.0 18.1 + - + +
598A GLY* 3.7 4.9 + - - -
600A GLU* 1.3 90.4 - - + +
602A ASP* 1.3 76.1 + - - +
731A HIS* 3.5 9.0 + - - -
84B LYS* 4.2 9.9 - - - +
87B GLN* 4.9 16.1 + - - +
99B ARG* 4.8 20.9 + - - +
102B GLY 5.8 3.6 - - - +
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Residues in contact with ASP 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A TRP* 3.1 29.0 + - + +
555A ASN* 3.8 10.7 + - - +
598A GLY* 2.9 16.0 + - - +
601A THR* 1.3 92.0 + - - +
603A GLY* 1.3 63.2 + - - +
731A HIS* 3.6 5.0 + - - -
733A ARG* 3.7 8.7 + - - -
84B LYS* 2.9 36.7 + - - +
87B GLN* 4.6 8.0 - - - +
92B PRO* 5.9 3.3 - - - +
99B ARG* 5.8 0.7 + - - -
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Residues in contact with GLY 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A TRP* 3.7 17.5 - - - +
599A ILE* 2.8 26.7 + - - -
602A ASP* 1.3 86.4 - - - +
604A SER* 1.3 64.0 + - - -
605A ASN* 4.5 1.9 - - - +
727A GLY 3.5 6.7 - - - -
731A HIS* 3.4 15.1 - - - -
733A ARG* 3.9 4.5 - - - -
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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