Contacts of the strand formed by residues 547 - 556 (chain J) in PDB entry 6ALH
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 ARG 547 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516J ASP* 3.4 39.0 + - + +
517J CYS 4.6 4.3 + - - +
518J VAL* 3.6 38.2 + - - +
523J GLU* 2.9 49.8 + - - +
524J GLY* 3.9 4.3 + - - -
546J ALA* 1.3 67.6 - - - +
548J VAL* 1.3 59.4 + - - +
571J ASP* 3.8 18.8 + - - +
572J THR 3.0 11.4 - - - +
573J THR* 4.5 7.2 - - + +
714J GLU* 5.3 1.8 + - - -
716J GLN* 5.3 1.4 + - - -
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Residues in contact with VAL 548 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522J GLY 3.5 24.5 - - - +
524J GLY* 4.2 5.4 - - - +
525J MET* 3.3 20.9 - - + +
527J LEU* 3.8 17.0 - - + -
546J ALA* 3.0 19.0 + - + +
547J ARG* 1.3 77.0 - - - +
549J LYS* 1.3 67.8 + - - +
550J VAL* 3.7 16.2 - - + -
571J ASP* 3.5 4.7 + - - -
572J THR* 2.8 35.5 + - + +
574J VAL* 3.8 17.5 - - + -
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Residues in contact with LYS 549 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H LEU* 5.4 8.3 - - + -
83H LEU* 5.8 0.2 - - - +
525J MET 3.8 3.8 + - - +
526J VAL* 3.4 38.3 - - + +
527J LEU 3.5 1.4 + - - -
548J VAL* 1.3 72.9 - - - +
550J VAL* 1.3 60.5 + - - +
569J LEU* 4.5 23.4 - - + +
570J LYS 3.3 7.8 - - - +
571J ASP* 4.4 28.5 + - + +
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Residues in contact with VAL 550 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H LEU* 5.0 1.1 - - - -
527J LEU* 3.3 33.9 - - + +
529J GLY 5.4 3.8 - - - +
530J PRO* 6.1 1.1 - - + -
533J ALA* 5.9 2.5 - - + -
548J VAL* 3.6 17.0 + - + +
549J LYS* 1.3 77.8 - - - +
551J ARG* 1.3 70.2 + - - +
552J ILE* 4.1 13.9 + - + -
569J LEU* 3.2 11.4 - - - -
570J LYS* 2.9 34.8 + - + +
572J THR* 3.7 23.6 - - + -
574J VAL* 6.1 2.7 - - + -
577J ALA* 4.6 13.2 - - + -
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Residues in contact with ARG 551 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H GLU* 3.4 38.8 + - - +
83H LEU* 4.0 23.2 - - + +
84H ASN* 3.3 30.5 + - - +
527J LEU 3.1 5.9 + - - -
528J THR* 3.5 33.9 + - - +
529J GLY* 3.9 11.4 - - - -
530J PRO* 4.0 4.5 - - - +
550J VAL* 1.3 77.1 - - - +
552J ILE* 1.3 69.2 + - - +
553J THR* 4.8 3.8 - - - +
567J THR* 3.4 28.6 + - - +
568J SER* 3.4 11.7 + - - +
569J LEU* 4.6 5.3 - - + +
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Residues in contact with ILE 552 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530J PRO* 4.8 10.1 - - + -
550J VAL* 4.1 15.9 - - + -
551J ARG* 1.3 80.5 - - - +
553J THR* 1.3 69.5 + - - +
554J GLU* 4.3 9.6 - - + +
567J THR* 2.3 33.7 + - - -
568J SER 3.7 4.9 + - - +
570J LYS* 3.7 40.4 - - + +
577J ALA* 5.6 2.5 - - + -
580J TRP* 4.5 18.6 - - + +
589J TYR* 3.8 46.7 - - + +
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Residues in contact with THR 553 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551J ARG* 4.8 4.2 - - - +
552J ILE* 1.3 86.2 + - - +
554J GLU* 1.3 64.2 + - - +
555J TYR* 4.0 29.4 - - + +
565J ALA* 4.6 8.5 - - + -
566J LYS 3.4 18.8 - - - +
567J THR* 3.4 11.8 + - + +
580J TRP* 3.6 20.2 + - - +
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Residues in contact with GLU 554 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552J ILE* 4.3 9.5 - - + +
553J THR* 1.3 76.7 - - - +
555J TYR* 1.3 70.2 + - - +
556J GLU* 4.1 6.6 - - + +
564J VAL 3.8 0.2 - - - +
565J ALA* 3.4 4.2 - - - -
566J LYS* 2.9 70.0 + - + +
567J THR* 5.9 0.2 - - - -
570J LYS* 5.4 6.6 + - - -
580J TRP* 4.4 14.4 - - + -
585J LYS 5.1 0.2 - - - -
587J LEU 4.6 6.3 - - - +
588J PRO* 3.5 9.5 - - + +
589J TYR* 2.9 33.5 + - - +
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Residues in contact with TYR 555 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J THR* 4.0 28.5 - - + +
554J GLU* 1.3 80.8 - - - +
556J GLU* 1.3 61.3 + - - +
557J LYS 4.0 0.2 + - - -
563J LEU* 4.2 26.2 - - + -
564J VAL 3.4 5.4 - - - +
565J ALA* 3.6 28.4 - - + +
580J TRP* 6.2 0.7 - + - -
585J LYS* 3.3 77.3 + - + +
586J GLY* 3.4 18.2 - - - +
587J LEU 4.7 1.1 + - - +
588J PRO* 5.9 0.8 - - - +
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Residues in contact with GLU 556 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554J GLU* 4.1 6.9 - - + +
555J TYR* 1.3 73.6 - - - +
557J LYS* 1.3 61.7 + - - +
558J ASP* 3.4 33.0 + - + +
562J GLU 3.6 0.7 - - - +
563J LEU* 4.7 0.4 - - - -
564J VAL* 2.9 40.2 + - + +
566J LYS* 4.7 18.9 + - + +
586J GLY 5.1 2.2 - - - -
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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