Contacts of the helix formed by residues 795 - 806 (chain B) in PDB entry 5YWB
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 ASN 795 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793B PRO* 3.5 13.9 + - - +
794B PHE* 1.3 94.3 - - - +
796B LYS* 1.3 68.8 + - - +
798B ARG* 3.4 31.3 - - + +
799B TYR* 3.3 20.1 + - - +
845B TYR* 4.0 5.2 + - - +
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Residues in contact with LYS 796 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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795B ASN* 1.3 76.1 - - - +
797B GLN* 1.3 81.6 + - + +
799B TYR* 4.7 0.7 - - - +
800B LYS* 3.6 28.6 + - + +
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Residues in contact with GLN 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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795B ASN* 3.5 0.6 - - - +
796B LYS* 1.3 102.2 - - + +
798B ARG* 1.3 60.9 + - - +
800B LYS* 3.4 16.5 + - - +
801B MET* 2.9 49.9 + - + +
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Residues in contact with ARG 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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795B ASN* 3.4 25.1 + - + +
796B LYS 3.5 0.4 - - - -
797B GLN* 1.3 78.5 - - - +
799B TYR* 1.3 62.5 + - - +
801B MET* 3.2 5.8 + - - +
802B VAL* 3.0 34.6 + - - +
844B LEU 4.0 6.8 + - - -
845B TYR* 2.9 51.5 + - + +
846B GLN 3.5 1.0 + - - -
847B GLN* 2.4 38.0 + - - +
876B LEU* 5.4 10.5 - - - +
880B ASP* 4.0 16.6 + - - -
882B ARG* 3.3 15.4 - - - +
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Residues in contact with TYR 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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784B VAL* 5.2 1.9 - - - +
785B GLU* 3.5 26.9 + - + +
788B ILE* 4.4 19.4 - - + +
789B THR* 5.2 2.7 - - + -
794B PHE* 3.9 29.8 - + + -
795B ASN 3.3 17.9 + - - +
796B LYS 5.4 0.4 - - - -
798B ARG* 1.3 79.2 - - - +
800B LYS* 1.3 69.4 + - + +
802B VAL* 3.3 2.1 + - + +
803B ILE* 2.9 67.5 + - + +
812B ILE* 5.8 1.6 - - - +
819B ASP* 3.1 24.1 + - - -
845B TYR* 3.9 21.0 - + + -
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Residues in contact with LYS 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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796B LYS* 3.6 22.3 + - + +
797B GLN* 3.4 19.9 + - - +
798B ARG 3.3 0.6 - - - -
799B TYR* 1.3 89.8 - - + +
801B MET* 1.3 58.3 + - - +
803B ILE* 3.4 4.1 + - - +
804B GLU* 2.9 60.1 + - - +
809B GLN* 4.0 15.0 - - - +
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Residues in contact with MET 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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797B GLN* 2.9 36.2 + - + +
798B ARG* 3.2 6.3 + - - +
800B LYS* 1.3 77.7 - - - +
802B VAL* 1.3 59.0 + - + +
804B GLU* 3.3 17.3 + - + +
805B ALA* 2.9 38.4 + - + +
876B LEU* 4.7 22.2 - - + -
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Residues in contact with VAL 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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788B ILE* 4.5 5.8 - - + -
798B ARG* 3.0 26.0 + - + +
799B TYR 3.3 3.3 + - - +
801B MET* 1.3 75.8 - - + +
803B ILE* 1.3 61.9 + - - +
805B ALA* 3.6 1.9 + - - +
806B CYS* 3.2 27.0 + - - -
841B ALA* 3.6 37.0 - - + +
844B LEU* 4.6 9.0 - - + +
845B TYR* 3.8 36.1 - - + +
876B LEU* 4.5 17.9 - - + -
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Residues in contact with ILE 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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784B VAL* 5.6 0.4 - - + -
788B ILE* 3.6 32.1 - - + -
799B TYR* 2.9 52.4 + - + +
800B LYS* 3.7 5.8 - - - +
802B VAL* 1.3 79.2 - - + +
804B GLU* 1.3 62.5 + - + +
805B ALA 3.1 0.2 - - - -
806B CYS* 3.2 14.8 + - - +
807B SER 3.8 6.6 + - - -
808B LEU* 3.8 21.7 + - + +
809B GLN* 3.8 39.3 + - + +
812B ILE* 5.5 7.6 - - + -
841B ALA* 5.6 1.3 - - + -
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Residues in contact with GLU 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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800B LYS* 2.9 50.5 + - - +
801B MET* 3.7 18.4 - - + +
803B ILE* 1.3 77.2 - - + +
805B ALA* 1.3 57.4 + - - +
807B SER* 4.6 2.7 + - - -
809B GLN* 4.1 28.1 + - + +
867B HIS* 3.8 15.4 + - - -
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Residues in contact with ALA 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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801B MET* 2.9 21.4 + - + +
802B VAL* 4.1 3.6 - - - +
803B ILE 3.1 0.2 - - - -
804B GLU* 1.3 78.1 - - - +
806B CYS* 1.3 59.9 + - - +
807B SER 3.3 5.6 + - - -
844B LEU* 5.4 1.3 - - + -
867B HIS* 3.9 13.4 + - - -
868B LEU* 3.6 17.8 - - - +
871B ALA* 4.1 23.2 - - + +
872B GLY* 4.3 10.5 - - - +
876B LEU* 4.3 16.4 - - + -
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Residues in contact with CYS 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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802B VAL* 3.2 25.3 + - - +
803B ILE* 3.2 6.7 + - - +
805B ALA* 1.3 77.0 - - - +
807B SER* 1.3 72.2 + - - +
808B LEU* 3.2 11.1 - - + +
837B ARG* 3.1 26.4 - - + +
840B VAL* 4.6 2.2 - - - -
841B ALA* 3.5 39.5 - - + -
844B LEU* 4.5 10.1 - - - -
868B LEU* 3.9 20.6 - - + +
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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