Contacts of the helix formed by residues 548 - 560 (chain W) in PDB entry 5O9G
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 ASN 548 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519W LYS* 5.2 2.3 - - - +
545W LEU 4.4 9.8 - - - +
546W GLN 3.4 2.7 - - - -
547W ASN* 1.3 110.1 + - - +
549W ILE* 1.3 64.3 + - - +
550W LYS* 4.2 9.6 - - + +
551W GLU* 3.2 34.7 + - + +
552W LEU 4.0 3.1 + - - -
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Residues in contact with ILE 549 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545W LEU 5.9 0.4 - - - +
548W ASN* 1.3 70.9 - - - +
550W LYS* 1.3 76.0 + - + +
551W GLU 3.1 1.1 - - - -
552W LEU* 3.5 13.5 + - + +
553W ALA* 2.9 37.2 + - + +
574W ASN 5.8 7.2 - - - +
582W TYR* 3.4 42.4 - - + +
586W LEU* 4.2 11.4 - - + -
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Residues in contact with LYS 550 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519W LYS 4.1 8.2 - - - +
520W ASN* 5.6 6.7 - - - +
521W ALA* 5.4 14.4 + - - +
548W ASN* 3.2 7.5 - - + -
549W ILE* 1.3 89.3 - - + +
551W GLU* 1.3 50.8 + - + +
553W ALA* 4.4 9.3 - - + +
554W ALA* 2.7 38.2 + - - +
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Residues in contact with GLU 551 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516W HIS* 4.3 2.1 - - - -
518W LEU 5.0 0.8 - - - +
519W LYS* 3.3 49.9 - - + +
543W THR* 3.9 10.2 + - - -
544W PRO* 2.9 25.3 - - - +
545W LEU* 3.7 11.7 - - + -
547W ASN* 3.1 24.9 + - - +
548W ASN* 3.2 29.7 - - + +
549W ILE 3.1 0.8 - - - -
550W LYS* 1.3 75.1 - - + +
552W LEU* 1.3 61.8 + - - +
554W ALA* 3.2 3.4 + - - +
555W LEU* 2.9 33.3 + - - +
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Residues in contact with LEU 552 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398W ILE* 6.0 2.5 - - + -
545W LEU* 3.7 49.6 - - + +
546W GLN* 5.5 4.5 - - - +
548W ASN 4.0 2.5 + - - +
549W ILE* 3.5 14.2 + - + +
551W GLU* 1.3 78.4 - - - +
553W ALA* 1.3 59.1 + - - +
555W LEU* 3.1 5.4 + - + -
556W VAL* 2.9 44.2 + - + +
583W ILE* 5.8 4.5 - - + -
586W LEU* 3.8 33.2 - - + -
590W ILE* 4.7 20.4 - - + -
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Residues in contact with ALA 553 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549W ILE* 2.9 29.5 + - + +
550W LYS* 4.4 10.1 - - + +
552W LEU* 1.3 77.5 - - - +
554W ALA* 1.3 56.9 + - - +
556W VAL* 3.1 9.4 + - - +
557W ASN* 2.9 39.8 + - - +
564W PHE 5.1 13.0 - - - -
582W TYR* 6.0 0.4 - - - +
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Residues in contact with ALA 554 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518W LEU 4.1 17.9 - - - +
519W LYS 4.7 2.5 - - - +
521W ALA* 4.6 12.1 - - + +
526W TYR* 2.7 32.0 + - + +
550W LYS 2.7 24.1 + - - +
551W GLU* 3.2 5.8 + - - +
553W ALA* 1.3 77.8 - - - +
555W LEU* 1.3 57.3 + - - +
557W ASN* 2.8 14.2 - - - +
558W PHE* 2.8 13.2 + - - +
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Residues in contact with LEU 555 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398W ILE* 3.8 35.3 - - + +
515W ALA* 4.8 7.4 - - + +
518W LEU* 4.5 29.4 - - + +
539W LEU* 3.7 22.4 - - + +
541W THR* 5.2 4.0 - - + -
543W THR* 4.2 12.3 - - + -
545W LEU* 3.7 35.2 - - + -
551W GLU 2.9 15.8 + - - +
552W LEU* 3.1 9.4 + - + +
554W ALA* 1.3 77.7 - - - +
556W VAL* 1.3 64.0 + - - +
558W PHE* 4.0 7.6 + - + +
559W LEU* 4.1 11.3 + - - +
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Residues in contact with VAL 556 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398W ILE* 6.4 0.9 - - + -
552W LEU* 2.9 29.1 + - + +
553W ALA* 3.1 9.3 + - - +
555W LEU* 1.3 80.0 - - - +
557W ASN* 1.3 59.8 + - - +
558W PHE 3.2 0.2 - - - -
559W LEU* 3.6 2.1 + - - +
560W MET* 2.9 30.4 + - + +
563W ARG* 3.7 33.9 - - + +
564W PHE 3.4 26.9 - - - +
586W LEU* 5.8 4.0 - - + -
590W ILE* 4.1 24.7 - - + -
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Residues in contact with ASN 557 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521W ALA* 5.9 3.2 - - - +
526W TYR* 2.5 30.8 + - - -
550W LYS* 6.0 2.6 - - - +
553W ALA* 2.9 25.6 + - - +
554W ALA* 2.8 16.0 - - - +
556W VAL* 1.3 75.9 - - - +
558W PHE* 1.3 64.3 + - - +
559W LEU 3.3 0.6 + - - -
560W MET 3.4 13.0 - - - +
561W PRO* 3.7 24.6 - - + +
562W GLY 4.9 2.0 - - - +
563W ARG 4.6 11.1 + - - +
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Residues in contact with PHE 558 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510W MET* 5.0 4.9 - - - -
518W LEU* 3.7 27.8 - - + -
526W TYR* 3.4 32.8 - + + +
529W LEU* 3.9 29.2 - - + -
530W ASN* 3.2 27.1 - - - +
537W ARG* 2.6 55.8 + - - -
539W LEU* 4.0 29.4 - - + -
554W ALA 2.8 22.9 + - - +
555W LEU* 4.1 6.7 - - + -
556W VAL 3.2 0.4 - - - -
557W ASN* 1.3 79.6 + - - +
559W LEU* 1.3 57.3 + - + +
561W PRO* 5.1 3.3 - - - +
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Residues in contact with LEU 559 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396W ASN* 4.2 34.7 + - + +
398W ILE* 6.4 1.3 - - + -
537W ARG* 4.6 12.8 - - + +
539W LEU* 5.8 4.5 - - + -
555W LEU 4.1 9.9 + - - +
556W VAL 3.6 2.0 + - - +
558W PHE* 1.3 87.4 - - + +
560W MET* 1.3 72.6 + - + +
561W PRO* 3.6 9.1 - - - +
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Residues in contact with MET 560 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394W GLY 4.6 2.5 - - - +
395W ASP* 3.7 24.5 - - + +
396W ASN* 3.5 40.2 - - + +
556W VAL* 2.9 20.5 + - + +
557W ASN* 3.4 6.4 - - - -
559W LEU* 1.3 89.6 - - + +
561W PRO* 1.3 67.9 - - - +
562W GLY 3.1 4.0 + - - -
563W ARG* 3.5 42.4 + - + +
593W PHE* 5.6 4.9 - - + -
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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