Contacts of the helix formed by residues 619 - 628 (chain O) in PDB entry 6LTJ
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 ASP 619 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616O TYR* 4.2 6.6 + - + +
617O LYS 3.8 0.8 - - - -
618O ASP* 1.3 74.5 - - - +
620O TRP* 1.3 60.9 + - - +
621O ASN* 3.1 27.4 + - - +
622O LYS* 3.2 42.8 + - + +
623O VAL* 3.2 20.8 + - - +
502P ARG* 3.6 29.5 + - - +
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Residues in contact with TRP 620 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412I PHE* 4.7 1.8 - + - -
416I LEU* 4.0 22.2 - - + -
609O LEU* 4.9 0.4 - - + -
613O LEU* 3.7 32.5 - - + -
618O ASP* 2.9 47.4 + - - -
619O ASP* 1.3 71.4 + - - +
621O ASN* 1.3 59.3 + - - +
623O VAL* 3.6 23.4 - - + +
624O SER* 2.9 21.8 + - - -
632O GLN* 3.4 20.4 - - + +
635O CYS* 4.3 11.4 - - + +
636O ILE* 3.5 46.7 - - + -
639O PHE* 4.0 17.3 - + - -
494P TYR* 3.1 17.2 + + - -
495P PHE* 4.1 24.0 - + + -
498P LYS* 5.0 6.7 - - + -
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Residues in contact with ASN 621 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423N HIS* 5.2 8.3 + - - -
532O HIS* 5.4 1.2 - - - -
619O ASP* 3.1 15.5 + - - +
620O TRP* 1.3 76.4 - - - +
622O LYS* 1.3 62.1 + - + +
624O SER* 3.2 4.4 + - - -
625O GLU* 2.9 41.5 + - + +
632O GLN* 2.3 28.8 + - - +
495P PHE* 4.7 9.7 - - - -
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Residues in contact with LYS 622 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616O TYR* 3.4 49.7 - - + -
619O ASP* 3.2 32.1 + - + +
621O ASN* 1.3 76.2 - - + +
623O VAL* 1.3 57.4 + - - +
625O GLU* 3.6 14.6 - - - +
626O HIS* 2.9 30.1 + - - +
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Residues in contact with VAL 623 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609O LEU* 3.8 29.8 - - + -
612O ALA* 3.9 21.1 - - + +
613O LEU* 4.4 8.1 - - + -
616O TYR* 3.3 24.7 - - + +
617O LYS 4.7 0.9 - - - +
619O ASP 3.2 15.9 + - - +
620O TRP* 3.6 30.5 - - + +
621O ASN 3.1 0.6 - - - -
622O LYS* 1.3 77.2 - - - +
624O SER* 1.3 57.5 + - - +
626O HIS* 3.2 2.8 + - - +
627O VAL* 2.9 34.8 + - + +
635O CYS* 4.5 3.1 - - + -
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Residues in contact with SER 624 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532O HIS* 3.4 22.3 + - - -
620O TRP 2.9 16.3 + - - -
621O ASN* 3.2 9.2 + - - -
623O VAL* 1.3 77.7 - - - +
625O GLU* 1.3 60.6 + - - +
627O VAL* 4.5 0.4 - - - -
628O GLY* 2.8 24.4 + - - -
630O ARG 3.8 17.9 - - - +
631O THR 3.9 8.3 - - - -
632O GLN* 3.6 15.7 - - - +
635O CYS* 4.3 11.0 - - - -
81R LYS* 3.4 8.4 + - - -
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Residues in contact with GLU 625 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532O HIS* 5.9 1.6 - - - +
621O ASN* 2.9 28.4 + - - +
622O LYS* 3.6 13.9 + - - +
624O SER* 1.3 75.9 - - - +
626O HIS* 1.3 68.4 + - - +
628O GLY* 3.0 15.7 + - - -
81R LYS* 4.7 6.5 - - + +
82R LYS* 5.2 17.0 - - - +
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Residues in contact with HIS 626 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608O LEU* 3.5 55.0 + - + +
611O GLU* 4.1 26.5 - - + -
612O ALA* 3.5 18.9 - - + +
615O MET* 4.1 22.7 - - + +
616O TYR* 4.2 10.5 - + + -
622O LYS 2.9 17.6 + - - +
625O GLU* 1.3 74.8 - - - +
627O VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 627 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601O TRP* 4.5 3.4 - - + -
605O GLU* 4.2 24.2 - - + +
608O LEU* 3.8 22.0 - - + +
609O LEU* 3.7 32.1 - - + +
623O VAL* 2.9 18.4 + - + +
624O SER 4.1 3.1 - - - +
626O HIS* 1.3 79.0 - - - +
628O GLY* 1.3 57.4 + - - +
629O SER* 2.9 18.7 + - - +
630O ARG* 4.1 22.2 - - + +
635O CYS* 4.1 16.6 - - - -
80R ARG* 5.3 3.6 - - - +
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Residues in contact with GLY 628 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624O SER 2.8 19.1 + - - -
625O GLU 3.0 13.9 + - - -
627O VAL* 1.3 70.7 - - - +
629O SER* 1.3 56.1 + - - +
630O ARG 3.6 2.0 - - - -
79R TRP* 3.2 8.4 - - - -
80R ARG* 3.3 7.9 - - - -
81R LYS* 2.7 43.3 + - - -
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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