Contacts of the helix formed by residues 795 - 809 (chain D) in PDB entry 5LSW
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 SER 795 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794D ASP* 1.3 76.1 - - - +
796D GLY* 1.3 59.9 + - - +
798D MET* 3.7 6.4 - - - +
799D LEU* 2.8 33.8 + - - +
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Residues in contact with GLY 796 (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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794D ASP* 3.2 7.5 + - - -
795D SER* 1.3 82.2 + - - +
797D MET* 1.3 55.5 + - - +
799D LEU* 3.4 5.1 + - - +
800D GLN* 2.9 32.3 + - - +
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Residues in contact with MET 797 (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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88C ASN* 3.3 24.2 - - - +
92C ASN* 6.1 0.4 - - - +
134C TYR* 3.5 37.7 + - + +
792D GLY 3.3 27.4 - - - +
793D ILE* 4.0 7.6 - - + -
794D ASP* 2.9 36.9 + - - +
796D GLY* 1.3 74.8 - - - +
798D MET* 1.3 63.3 + - - +
800D GLN* 3.4 5.7 + - - +
801D LEU* 3.0 24.6 + - - +
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Residues in contact with MET 798 (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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130C ARG* 5.4 11.0 - - + +
133C GLU* 4.2 15.0 - - + -
134C TYR* 3.9 28.2 - - - +
137C LEU* 3.8 26.7 - - + -
177C LEU* 5.9 2.0 - - + -
793D ILE* 4.8 8.3 - - + +
794D ASP 3.1 15.7 + - - +
795D SER* 3.7 7.4 - - - +
797D MET* 1.3 76.9 - - - +
799D LEU* 1.3 62.5 + - - +
801D LEU* 3.3 10.2 + - - +
802D GLU* 3.1 20.8 + - - +
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Residues in contact with LEU 799 (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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795D SER 2.8 22.1 + - - +
796D GLY* 3.9 5.2 - - - +
798D MET* 1.3 72.5 - - - +
800D GLN* 1.3 62.8 + - - +
802D GLU* 3.2 25.6 + - + +
803D LYS* 3.0 53.6 + - + +
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Residues in contact with GLN 800 (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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47C GLU* 3.8 21.4 + - - -
796D GLY 2.9 19.4 + - - +
797D MET* 3.8 6.1 - - - +
799D LEU* 1.3 77.8 - - - +
801D LEU* 1.3 61.7 + - - +
803D LYS* 3.4 21.5 + - - +
804D ASN* 3.0 26.5 + - + +
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Residues in contact with LEU 801 (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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134C TYR* 3.7 25.6 - - + +
137C LEU* 3.5 31.6 - - + +
138C THR* 3.6 36.1 - - + +
177C LEU* 5.8 0.2 - - + -
797D MET 3.0 13.8 + - - +
798D MET* 3.5 10.3 - - - +
800D GLN* 1.3 78.3 - - - +
802D GLU* 1.3 62.7 + - - +
804D ASN* 3.1 18.4 + - - +
805D LEU* 2.9 47.5 + - + +
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Residues in contact with GLU 802 (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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177C LEU* 3.9 32.0 - - + +
227C ARG* 3.9 19.9 + - - -
798D MET 3.1 12.8 + - - +
799D LEU* 3.2 28.5 + - + +
801D LEU* 1.3 75.9 - - - +
803D LYS* 1.3 59.7 + - + +
805D LEU* 3.2 2.8 + - - +
806D VAL* 2.9 43.2 + - + +
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Residues in contact with LYS 803 (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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799D LEU* 3.0 46.1 + - + +
800D GLN* 3.8 23.2 + - - +
801D LEU 3.3 0.2 - - - -
802D GLU* 1.3 76.4 - - + +
804D ASN* 1.3 62.2 + - - +
806D VAL* 3.9 5.9 - - - +
807D ASP* 3.0 37.5 + - - +
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Residues in contact with ASN 804 (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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46C ARG* 3.5 22.0 + - - +
98C GLN* 3.3 37.1 + - - +
141C GLY* 5.0 0.8 - - - -
800D GLN* 3.0 17.8 + - + +
801D LEU* 3.1 24.5 + - - +
803D LYS* 1.3 77.7 - - - +
805D LEU* 1.3 66.0 + - - +
807D ASP* 3.4 6.2 + - - +
808D ILE* 3.1 29.8 + - - +
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Residues in contact with LEU 805 (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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137C LEU* 3.7 46.4 - - + +
141C GLY* 3.5 33.0 - - - +
177C LEU* 4.0 20.2 - - + -
181C VAL* 4.0 23.3 - - + -
801D LEU* 2.9 29.5 + - + +
802D GLU 3.7 4.0 - - - +
804D ASN* 1.3 77.1 - - - +
806D VAL* 1.3 66.2 + - - +
808D ILE* 3.1 7.7 + - + +
809D VAL* 3.1 29.9 + - - +
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Residues in contact with VAL 806 (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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274A ARG* 4.1 15.3 - - - +
177C LEU* 4.7 4.5 - - + -
227C ARG* 3.5 31.9 - - - +
802D GLU* 2.9 28.3 + - + +
803D LYS* 3.9 7.0 - - - +
805D LEU* 1.3 74.8 - - - +
807D ASP* 1.3 64.2 + - - +
809D VAL* 4.2 7.4 - - + -
810D ASP* 3.0 46.8 + - + +
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Residues in contact with ASP 807 (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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278A GLN* 3.1 43.7 + - - +
148C LYS* 2.9 19.9 + - - +
803D LYS* 3.0 24.8 + - - +
804D ASN* 3.8 7.0 + - - +
806D VAL* 1.3 83.1 - - - +
808D ILE* 1.3 60.9 + - + +
810D ASP* 3.3 14.0 - - - +
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Residues in contact with ILE 808 (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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98C GLN* 4.0 6.5 - - - +
141C GLY* 3.5 33.0 - - - +
144C GLY* 3.7 28.3 - - - +
145C ALA* 4.0 15.9 - - + +
148C LYS* 3.3 31.7 - - + +
181C VAL* 5.7 2.2 - - + -
184C PHE* 3.6 17.5 - - + -
804D ASN* 3.1 30.1 + - - +
805D LEU* 3.1 12.4 + - + +
807D ASP* 1.3 78.5 - - + +
809D VAL* 1.3 66.8 + - + +
810D ASP 3.6 0.3 + - - -
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Residues in contact with VAL 809 (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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180C THR* 4.1 15.9 - - + +
181C VAL* 4.1 25.1 - - + -
184C PHE* 3.7 43.0 - - + -
227C ARG* 5.8 1.3 - - + -
231C HIS* 3.1 32.6 - - - +
805D LEU 3.1 16.8 + - - +
806D VAL* 3.7 9.2 - - + +
808D ILE* 1.3 79.8 - - + +
810D ASP* 1.3 75.9 + - - +
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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