Contacts of the strand formed by residues 705 - 712 (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 ASP 705 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288D ARG* 2.9 14.4 + - - -
296D LEU* 3.5 24.1 - - + +
297D HIS* 2.8 36.3 + - - -
519D ASN* 4.8 2.9 + - - -
701D MET* 3.5 3.0 - - - +
702D VAL* 2.8 44.0 + - - +
703D ASN 4.4 4.3 - - - +
704D GLY* 1.3 78.6 - - - +
706D HIS* 1.3 61.2 + - - +
707D ARG* 3.8 19.0 + - + +
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Residues in contact with HIS 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ASN* 4.3 4.9 + - - -
517D VAL* 3.4 26.9 - - + +
518D TYR 3.5 20.6 - - - -
519D ASN* 3.1 24.6 + - - +
541D ASN* 5.2 1.2 + - - -
645D ILE* 5.0 2.4 - - - +
669D LEU* 3.5 41.0 - - + +
670D ASN* 3.5 13.1 + - + +
699D VAL* 4.4 7.4 - - + -
700D MET 3.5 11.9 - - - +
701D MET* 3.3 37.3 - - + +
704D GLY 4.2 0.2 + - - -
705D ASP* 1.3 72.2 - - - +
707D ARG* 1.3 64.5 - - - +
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Residues in contact with ARG 707 (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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117D GLN 4.5 5.9 + - - -
118D GLN* 4.6 15.1 - - - +
119D ASN* 4.6 6.8 - - - +
296D LEU* 6.3 1.7 - - - +
606D ILE* 3.4 44.2 + - + +
607D GLN* 3.6 18.8 + - - +
640D GLU* 2.6 39.0 + - - +
669D LEU* 3.9 5.0 - - - +
699D VAL* 4.3 1.1 - - - +
700D MET 3.1 27.9 + - - +
702D VAL* 3.9 23.1 - - + +
705D ASP* 3.8 24.7 + - + +
706D HIS* 1.3 80.0 - - - +
708D ILE* 1.3 64.2 + - - +
709D GLY 3.7 0.7 + - - -
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Residues in contact with ILE 708 (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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119D ASN* 5.0 0.4 - - - +
606D ILE* 4.7 0.7 - - - -
640D GLU* 3.1 15.7 + - - +
641D TYR* 2.9 56.2 + - + +
667D PHE* 4.3 22.9 - - + +
668D ASN 3.6 24.2 - - - +
669D LEU* 3.6 22.2 - - + -
675D VAL* 4.1 9.6 - - + -
697D ALA* 4.6 13.7 - - + -
698D LYS 4.4 6.7 - - - +
699D VAL* 4.5 12.3 - - + +
707D ARG* 1.3 71.1 - - - +
709D GLY* 1.3 61.9 + - - +
710D ILE* 4.5 9.6 - - + -
728D TYR 4.7 2.9 - - - +
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Residues in contact with GLY 709 (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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606D ILE* 4.1 14.1 - - - -
637D PHE* 4.6 2.2 - - - -
639D SER 4.2 2.7 - - - -
696D TYR 3.5 1.9 - - - +
697D ALA* 3.6 2.4 - - - -
698D LYS 3.1 29.1 + - - -
707D ARG 3.7 1.6 + - - -
708D ILE* 1.3 75.0 - - - +
710D ILE* 1.3 62.2 + - - -
711D PHE* 3.1 30.9 - - - -
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Residues in contact with ILE 710 (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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637D PHE* 3.8 2.5 - - - -
638D ILE* 2.7 34.7 + - + +
639D SER 2.9 23.3 + - - +
641D TYR* 3.9 36.1 - - + +
684D ILE* 4.2 28.3 - - + -
687D ALA* 5.9 1.1 - - + -
695D CYS* 4.0 22.2 - - + -
696D TYR 3.5 11.9 - - - +
697D ALA* 4.2 16.2 - - + -
708D ILE* 4.5 2.5 - - + -
709D GLY* 1.3 78.6 - - - +
711D PHE* 1.3 57.0 + - - +
722D LEU* 6.4 0.2 - - + -
724D PHE* 4.5 16.8 - - + -
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Residues in contact with PHE 711 (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* 5.4 4.0 - - - -
605D SER* 5.8 0.4 - - - -
606D ILE* 4.7 3.4 - - + -
635D ASN 4.2 9.6 - - - -
636D GLU 3.4 11.9 - - - +
637D PHE* 3.4 41.7 - + + -
638D ILE* 3.9 6.1 - - - -
695D CYS* 3.0 4.7 - - - +
696D TYR* 2.8 62.5 + + + +
698D LYS* 3.8 18.2 - - + -
700D MET* 4.1 22.7 - - - -
709D GLY* 3.1 36.3 - - - -
710D ILE* 1.3 72.5 - - - +
712D ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 712 (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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632D VAL* 4.4 6.5 - - + -
633D GLN 3.8 18.6 - - - +
635D ASN* 3.2 23.1 + - - +
636D GLU 3.3 9.6 + - - +
638D ILE* 3.8 5.1 - - + +
694D ASN 3.3 12.1 - - - +
695D CYS* 4.0 0.4 - - - +
696D TYR* 3.7 7.7 - - - -
711D PHE* 1.3 78.5 - - - +
713D LYS* 1.3 58.9 + - - +
714D ARG 3.3 22.0 - - - +
716D ILE* 3.8 11.7 - - + -
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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