Contacts of the strand formed by residues 695 - 702 (chain D) in PDB entry 5LS6
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 CYS 695 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638D ILE* 3.4 28.5 - - - -
693D PRO* 3.6 14.8 - - - +
694D ASN* 1.3 90.1 - - - +
696D TYR* 1.3 58.8 + - - +
710D ILE* 4.0 17.7 - - + -
711D PHE 3.0 14.1 - - - +
713D LYS* 3.9 8.6 - - - +
716D ILE* 4.3 0.2 - - - -
722D LEU* 3.5 27.4 - - - -
723D PHE 3.3 14.0 + - - +
724D PHE* 3.4 18.0 - - + +
725D ASP 4.8 0.2 + - - -
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Residues in contact with TYR 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D TYR* 5.0 5.0 + - - -
634D LYS* 6.3 0.2 - - - -
635D ASN* 3.1 44.8 + - - +
695D CYS* 1.3 76.6 - - - +
697D ALA* 1.3 62.7 + - - +
698D LYS* 4.4 24.6 + - + +
709D GLY 3.5 2.9 - - - +
710D ILE* 3.5 7.8 - - - +
711D PHE* 2.8 63.0 + + + +
712D ALA 3.7 9.2 - - - -
713D LYS* 4.2 27.6 - - + -
724D PHE* 4.6 5.2 - - - -
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Residues in contact with ALA 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D PHE* 6.1 0.9 - - + -
696D TYR* 1.3 76.1 - - - +
698D LYS* 1.3 59.7 + - - +
699D VAL* 4.2 3.3 + - + +
708D ILE* 4.6 10.3 - - + -
709D GLY 3.6 5.4 - - - -
710D ILE* 4.2 14.4 - - + -
724D PHE* 4.5 19.8 - - + +
725D ASP 5.4 2.2 - - - +
728D TYR 5.4 7.2 - - - +
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Residues in contact with LYS 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D TYR* 3.6 43.6 + - - -
577D VAL* 4.8 15.5 - - + +
696D TYR* 3.9 20.3 + - + +
697D ALA* 1.3 72.7 - - - +
699D VAL* 1.3 70.9 + - - +
700D MET* 3.8 25.4 + - + +
708D ILE* 5.0 1.1 - - - -
709D GLY* 3.1 29.1 + - - +
711D PHE* 3.8 20.2 - - + -
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Residues in contact with VAL 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D VAL* 3.2 21.5 - - - +
668D ASN 4.3 16.6 - - - +
669D LEU* 3.7 39.7 - - + +
697D ALA 4.2 2.9 + - - +
698D LYS* 1.3 75.3 - - - +
700D MET* 1.3 68.5 + - - +
706D HIS* 4.4 8.3 - - + -
707D ARG 4.1 9.4 - - - +
708D ILE* 4.5 12.1 - - + +
728D TYR 5.9 1.1 - - - +
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Residues in contact with MET 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D TYR* 5.1 6.5 - - + +
577D VAL* 4.0 15.7 - - + -
578D ARG 3.7 35.4 - - - +
579D GLU* 4.0 12.1 - - + +
603D ASN* 3.9 14.4 - - - +
606D ILE* 4.5 7.9 - - + -
698D LYS* 3.8 26.0 - - + +
699D VAL* 1.3 83.7 - - - +
701D MET* 1.3 62.0 + - - +
702D VAL* 3.7 14.4 + - + +
706D HIS* 3.5 7.5 - - - +
707D ARG 3.1 32.7 + - - +
711D PHE* 4.1 24.5 - - - -
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Residues in contact with MET 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D TYR* 3.4 28.5 - - + -
541D ASN* 5.4 7.2 - - + +
544D GLU* 4.3 9.9 - - - +
577D VAL 3.3 16.0 + - - +
578D ARG* 3.3 34.9 + - + +
579D GLU 3.3 23.2 + - - +
700D MET* 1.3 71.1 - - - +
702D VAL* 1.3 61.9 + - - +
703D ASN 4.4 1.5 + - - +
704D GLY* 3.4 31.4 - - - +
705D ASP 3.5 9.0 - - - +
706D HIS* 3.3 36.1 - - + +
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Residues in contact with VAL 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579D GLU* 3.6 33.4 - - + +
606D ILE* 4.5 11.2 - - + -
607D GLN* 3.7 33.4 - - + +
700D MET* 4.3 12.3 - - + +
701D MET* 1.3 79.0 - - - +
703D ASN* 1.3 78.8 + - - +
704D GLY 3.3 1.3 - - - -
705D ASP* 2.8 28.8 + - - +
707D ARG* 3.9 26.3 - - + +
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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