Contacts of the helix formed by residues 853 - 863 (chain A) in PDB entry 2WXL
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 853 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A ALA* 4.0 8.1 - - + -
849A ALA* 5.5 1.2 - - - +
850A PHE* 2.9 20.5 + - - +
852A LYS* 1.3 98.8 + - - +
854A ALA* 1.3 58.2 + - - +
855A LEU 3.4 0.7 - - - -
856A LEU* 3.5 15.2 + - - +
857A ASN* 2.9 44.5 + - - +
860A LYS* 5.8 0.5 + - - -
940A HIS* 3.1 24.0 + - - -
945A GLY* 4.9 1.7 - - - +
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Residues in contact with ALA 854 (chain A).
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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837A ILE* 4.0 21.6 - - + +
838A GLN* 4.4 13.9 - - + -
840A ASN* 4.6 12.6 - - - +
846A ALA* 3.6 12.4 - - + +
848A ALA* 3.9 14.4 - - + +
851A ASN* 3.0 18.0 + - - +
852A LYS 3.3 0.2 - - - -
853A ASP* 1.3 76.9 - - - +
855A LEU* 1.3 58.8 + - - +
857A ASN 3.5 0.2 + - - -
858A TRP* 2.9 27.7 + - - +
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Residues in contact with LEU 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A ILE* 3.9 29.4 - - + -
837A ILE* 3.8 23.3 - - + +
838A GLN* 5.2 6.9 - - + +
851A ASN 4.7 0.4 + - - -
852A LYS 4.4 4.5 + - - +
853A ASP 3.4 0.4 - - - -
854A ALA* 1.3 75.3 - - - +
856A LEU* 1.3 59.5 + - - +
858A TRP* 3.1 5.6 + - + +
859A LEU* 2.8 34.6 + - + +
875A PHE* 4.1 11.7 - - + -
901A ILE* 4.1 24.5 - - + -
937A ASP* 4.3 10.3 - - + +
938A PHE* 4.1 29.6 - - + -
941A VAL* 4.0 22.0 - - + -
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Residues in contact with LEU 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A LYS 4.9 0.6 + - - -
853A ASP* 3.5 21.9 + - - +
855A LEU* 1.3 78.6 - - - +
857A ASN* 1.3 57.2 + - - +
859A LEU* 3.1 9.4 + - + +
860A LYS* 2.8 59.0 + - - +
868A LEU* 5.3 2.0 - - + -
872A ILE* 4.2 24.9 - - + -
940A HIS* 4.8 4.9 - - + +
941A VAL* 4.0 36.6 - - + +
944A GLN 4.0 4.3 - - - +
945A GLY* 3.6 32.1 - - - +
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Residues in contact with ASN 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A ALA 5.0 2.0 + - - +
846A ALA* 3.4 35.3 + - - +
847A THR 3.5 17.2 + - - -
848A ALA* 3.6 14.6 - - - +
853A ASP* 2.9 30.3 + - - +
854A ALA 3.6 2.9 - - - +
856A LEU* 1.3 72.0 - - - +
858A TRP* 1.3 62.9 + - - +
860A LYS* 3.3 23.9 + - - +
861A SER* 3.1 22.9 + - - -
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Residues in contact with TRP 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831A SER 5.4 0.7 - - - -
832A ASP* 4.7 12.6 + - + +
837A ILE* 3.6 38.7 - - + +
845A ALA* 6.5 0.2 - - + -
846A ALA* 3.4 14.7 - - + +
854A ALA 2.9 15.0 + - - +
855A LEU* 3.1 10.1 + - + +
857A ASN* 1.3 75.0 - - - +
859A LEU* 1.3 79.8 + - + +
861A SER* 2.7 22.5 + - - -
862A LYS* 3.2 35.5 + - + +
901A ILE* 3.6 31.0 - - + -
902A ARG 3.5 29.8 - - - -
903A GLU* 3.7 30.3 - - + -
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Residues in contact with LEU 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A LEU* 2.8 17.0 + - + +
856A LEU* 3.1 14.8 + - + +
858A TRP* 1.3 89.0 - - + +
860A LYS* 1.3 56.7 + - - +
862A LYS* 3.3 0.7 + - - -
863A ASN* 2.9 46.3 + - - +
868A LEU* 4.4 10.5 - - + -
871A ALA* 4.6 4.3 - - + +
872A ILE* 4.8 9.4 - - + +
875A PHE* 4.7 6.3 - - + -
901A ILE* 3.7 22.4 - - + -
905A GLY* 3.6 30.3 - - - +
941A VAL* 3.8 31.2 - - + -
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Residues in contact with LYS 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853A ASP* 5.8 0.4 + - - -
856A LEU* 2.8 42.3 + - - +
857A ASN* 3.5 25.3 + - - +
858A TRP 3.3 0.4 - - - -
859A LEU* 1.3 77.2 - - - +
861A SER* 1.3 60.8 + - - +
863A ASN 3.2 21.3 + - - +
864A PRO* 3.4 8.1 - - - +
868A LEU* 3.8 35.9 - - + -
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Residues in contact with SER 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A ALA* 3.6 33.6 - - - +
857A ASN 3.1 10.1 + - - -
858A TRP* 2.7 25.3 + - - -
860A LYS* 1.3 76.5 - - - +
862A LYS* 1.3 72.2 + - - +
864A PRO* 4.2 7.6 - - - +
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Residues in contact with LYS 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858A TRP* 3.2 50.9 + - + +
859A LEU* 3.9 1.6 - - - +
861A SER* 1.3 85.4 + - - +
863A ASN* 1.3 77.3 + - - +
864A PRO* 3.6 6.8 - - - +
903A GLU* 3.7 47.9 + - + +
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Residues in contact with ASN 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859A LEU* 2.9 27.0 + - - +
860A LYS* 3.2 7.5 - - - +
862A LYS* 1.3 86.2 - - - +
864A PRO* 1.3 69.4 - - - +
865A GLY 3.6 0.2 + - - -
867A ALA* 3.9 13.3 - - - +
868A LEU* 3.2 36.4 + - - +
871A ALA* 3.5 23.6 - - + +
903A GLU 2.9 27.5 + - - +
904A SER* 4.7 4.3 - - - +
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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