Contacts of the helix formed by residues 795 - 809 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.4 16.3 + - - +
794B ASP* 1.3 75.9 - - - +
796B GLY* 1.3 61.7 + - - +
798B MET* 3.6 3.0 + - - +
799B LEU* 3.2 22.2 + - - +
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Residues in contact with GLY 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B ASP* 3.0 8.7 + - - +
795B SER* 1.3 75.7 - - - +
797B MET* 1.3 59.5 + - - +
799B LEU* 3.0 9.5 + - - +
800B GLN* 2.9 28.7 + - - +
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Residues in contact with MET 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ASN* 3.3 33.2 - - - +
92A ASN* 5.7 0.7 - - - +
134A TYR* 3.4 33.2 + - + +
792B GLY 3.8 10.8 - - - +
793B ILE* 4.2 5.6 - - + -
794B ASP* 3.0 40.6 + - - +
796B GLY* 1.3 76.5 - - - +
798B MET* 1.3 62.6 - - - +
800B GLN* 3.3 6.3 + - - +
801B LEU* 3.1 24.3 + - - +
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Residues in contact with MET 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.5 42.2 - - + +
133A GLU* 3.7 22.0 - - + -
134A TYR* 3.7 30.8 - - - +
137A LEU* 3.7 30.1 - - + +
793B ILE* 4.7 2.7 - - + +
794B ASP 3.4 3.4 + - - +
795B SER 3.8 4.5 - - - +
796B GLY 3.2 0.6 - - - -
797B MET* 1.3 79.3 - - - +
799B LEU* 1.3 62.1 + - - +
801B LEU* 3.5 4.4 + - - +
802B GLU* 3.4 19.4 + - - +
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Residues in contact with LEU 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795B SER 3.2 10.7 + - - +
796B GLY* 3.0 11.9 + - - +
798B MET* 1.3 80.9 - - - +
800B GLN* 1.3 75.3 + - - +
802B GLU* 3.2 11.7 + - - +
803B LYS* 3.1 25.4 + - + +
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Residues in contact with GLN 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 5.3 4.9 - - - +
796B GLY 2.9 15.3 + - - +
797B MET* 3.3 7.8 + - - +
799B LEU* 1.3 85.8 - - - +
801B LEU* 1.3 61.3 + - - +
803B LYS* 3.2 39.2 + - - +
804B ASN* 3.0 22.2 + - + +
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Residues in contact with LEU 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.7 26.9 - - + +
137A LEU* 3.6 28.9 - - + -
138A THR* 3.3 38.4 - - + +
797B MET 3.1 16.5 + - - +
798B MET* 3.7 6.7 - - - +
799B LEU 3.2 0.4 - - - -
800B GLN* 1.3 76.8 - - - +
802B GLU* 1.3 57.4 + - - +
804B ASN* 3.1 20.9 + - + +
805B LEU* 2.9 49.8 + - + +
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Residues in contact with GLU 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 3.6 32.5 - - + +
227A ARG* 3.0 33.9 + - - +
798B MET 3.4 9.0 + - - +
799B LEU* 3.2 13.3 + - - +
801B LEU* 1.3 78.0 - - - +
803B LYS* 1.3 57.6 + - - +
805B LEU* 3.1 1.6 + - - +
806B VAL* 2.8 33.7 + - + +
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Residues in contact with LYS 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799B LEU* 3.1 20.3 + - + +
800B GLN* 3.2 39.4 + - - +
802B GLU* 1.3 77.4 - - - +
804B ASN* 1.3 61.4 + - - +
806B VAL* 3.5 4.8 + - - +
807B ASP* 3.1 42.1 + - - +
281C LYS* 4.5 29.2 - - - +
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Residues in contact with ASN 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 3.9 20.8 + - - +
98A GLN* 3.3 38.9 + - - +
141A GLY* 5.2 0.4 - - - -
800B GLN* 3.0 13.2 + - - +
801B LEU* 3.1 24.2 + - + +
803B LYS* 1.3 75.5 - - - +
805B LEU* 1.3 65.8 + - - +
807B ASP* 3.3 9.4 + - - +
808B ILE* 3.1 31.1 + - - +
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Residues in contact with LEU 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.7 47.1 - - + +
141A GLY* 3.5 32.3 - - - +
177A LEU* 3.8 22.0 - - + -
181A VAL* 4.2 22.2 - - + -
801B LEU* 2.9 30.6 + - + +
802B GLU* 3.7 4.7 - - - +
804B ASN* 1.3 75.0 - - - +
806B VAL* 1.3 62.0 + - - +
808B ILE* 3.3 8.7 + - + +
809B VAL* 2.8 34.9 + - - +
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Residues in contact with VAL 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 5.0 2.9 - - + -
227A ARG* 3.5 32.8 - - - +
802B GLU* 2.8 29.0 + - + +
803B LYS* 3.9 5.4 - - - +
805B LEU* 1.3 72.7 - - - +
807B ASP* 1.3 64.2 + - - +
809B VAL* 4.6 4.9 - - + -
810B ASP* 2.8 46.8 + - + +
274C ARG* 4.6 16.6 - - + +
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Residues in contact with ASP 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LYS* 3.6 10.8 + - - -
803B LYS* 3.1 31.4 + - - +
804B ASN* 3.3 10.9 + - - +
806B VAL* 1.3 82.2 - - - +
808B ILE* 1.3 62.8 + - + +
810B ASP 3.2 16.4 - - - +
278C GLN* 3.1 44.4 + - - +
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Residues in contact with ILE 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 3.8 12.8 - - - +
141A GLY* 3.7 27.4 - - - +
144A GLY* 3.6 32.3 - - - +
145A ALA* 3.8 9.9 - - + +
148A LYS* 3.0 32.2 + - + +
181A VAL* 5.8 2.5 - - + -
184A PHE* 3.6 16.2 - - + -
804B ASN* 3.1 37.0 + - - +
805B LEU* 3.6 9.0 - - + +
807B ASP* 1.3 77.7 - - + +
809B VAL* 1.3 65.9 + - + +
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Residues in contact with VAL 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A THR* 3.7 18.2 - - + +
181A VAL* 3.9 30.1 - - + +
184A PHE* 3.5 39.7 - - + -
227A ARG* 5.7 1.1 - - + -
231A HIS* 3.1 46.7 - - - +
805B LEU 2.8 19.4 + - - +
806B VAL* 4.1 3.1 - - + +
808B ILE* 1.3 78.0 - - + +
810B ASP* 1.3 70.5 + - - +
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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