Contacts of the helix formed by residues 956 - 969 (chain B) in PDB entry 4Q0W
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 956 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781B ARG* 2.7 21.7 + - - +
954B VAL* 3.3 4.6 + - - +
955B PRO* 1.3 70.5 - - - +
957B LEU* 1.3 57.0 + - - +
958B ASP* 3.4 12.3 + - - +
959B MET* 3.2 37.1 + - + +
960B LEU* 2.8 32.3 + - - +
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Residues in contact with LEU 957 (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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955B PRO 3.4 5.9 + - - -
956B ASP* 1.3 71.7 + - - +
958B ASP* 1.3 58.2 + - - +
960B LEU* 3.2 5.1 + - - -
961B ARG* 2.8 61.9 + - + +
976B ASP* 3.5 22.0 - - - +
979B LEU* 3.8 35.2 - - + -
980B ILE* 3.8 26.5 - - + +
983B ILE* 4.5 19.3 - - + -
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Residues in contact with ASP 958 (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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956B ASP* 3.3 8.4 + - - +
957B LEU* 1.3 82.4 - - - +
959B MET* 1.3 68.0 + - + +
961B ARG* 3.4 25.9 + - - +
962B SER* 3.2 21.2 + - - -
972B HIS* 5.5 0.7 - - - -
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Residues in contact with MET 959 (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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781B ARG* 2.8 69.7 + - + +
956B ASP* 3.2 32.2 + - + +
958B ASP* 1.3 82.4 - - + +
960B LEU* 1.3 61.1 + - - +
962B SER* 3.2 8.2 + - - +
963B PHE* 3.0 14.4 + - - +
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Residues in contact with LEU 960 (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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59B PHE* 5.3 1.3 - - + -
778B LEU* 3.8 15.9 - - + -
781B ARG* 3.7 34.1 - - + +
782B PHE* 3.7 35.0 - - + -
955B PRO* 3.9 15.9 - - + -
956B ASP 2.8 28.7 + - - +
957B LEU* 3.8 2.9 - - - +
959B MET* 1.3 75.1 - - - +
961B ARG* 1.3 68.2 + - - +
963B PHE* 4.2 2.5 - - + -
964B MET* 2.9 32.1 + - + +
979B LEU* 3.6 30.5 - - + -
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Residues in contact with ARG 961 (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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957B LEU* 2.8 48.9 + - + +
958B ASP* 3.4 21.5 + - - +
960B LEU* 1.3 74.2 - - - +
962B SER* 1.3 58.0 + - - +
964B MET* 4.0 1.4 - - - +
965B LYS* 3.0 29.5 + - - +
970B TRP 4.6 0.5 - - - +
972B HIS* 3.8 48.2 + - + +
975B SER* 4.4 11.8 + - - -
976B ASP* 2.7 45.7 + - - +
979B LEU* 5.0 0.6 - - - +
980B ILE* 5.1 2.0 - - - +
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Residues in contact with SER 962 (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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781B ARG* 3.7 7.3 + - - -
958B ASP 3.2 10.3 + - - -
959B MET* 3.2 23.9 + - - +
961B ARG* 1.3 77.6 - - - +
963B PHE* 1.3 58.8 + - - +
965B LYS* 3.6 6.5 - - - +
966B THR* 2.9 36.9 + - - -
972B HIS* 4.3 9.4 - - - -
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Residues in contact with PHE 963 (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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55B ILE* 4.0 20.9 - - + -
774B GLU* 3.5 23.1 - - - -
777B GLU* 3.6 21.3 - - + -
778B LEU* 3.9 32.5 - - + -
781B ARG* 3.6 31.6 - - - +
959B MET 3.0 19.7 + - - +
960B LEU* 3.3 5.8 + - - +
962B SER* 1.3 77.8 + - - +
964B MET* 1.3 64.8 + - - +
966B THR* 3.2 3.9 + - - -
967B GLN* 2.8 70.6 + - + +
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Residues in contact with MET 964 (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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55B ILE* 4.3 11.2 - - + -
59B PHE* 3.5 46.7 - - + -
778B LEU* 4.5 3.4 - - + -
960B LEU* 2.9 23.7 + - + +
963B PHE* 1.3 89.6 - - + +
965B LYS* 1.3 61.8 + - - +
967B GLN* 4.9 0.4 - - - -
968B LEU* 2.9 52.8 + - + +
969B GLY 3.2 4.7 + - - -
970B TRP* 3.4 34.7 + - + +
975B SER* 3.5 22.4 - - - +
979B LEU* 5.4 0.2 - - + -
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Residues in contact with LYS 965 (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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961B ARG 3.0 18.9 + - - +
962B SER* 3.6 9.0 - - - +
964B MET* 1.3 76.2 - - - +
966B THR* 1.3 61.8 + - - +
969B GLY* 2.8 30.5 + - - +
970B TRP 3.2 31.7 + - - +
971B PRO* 4.3 14.1 - - + +
972B HIS* 4.3 18.0 - - + +
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Residues in contact with THR 966 (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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962B SER* 2.9 25.2 + - - -
963B PHE* 3.7 4.9 - - - -
965B LYS* 1.3 81.0 - - - +
967B GLN* 1.3 76.9 + - - +
969B GLY 4.5 0.7 + - - -
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Residues in contact with GLN 967 (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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51B LYS* 5.7 1.0 - - - +
52B ASN* 2.8 33.9 + - - +
55B ILE* 3.3 30.1 - - + +
774B GLU* 3.8 22.4 + - - +
963B PHE* 2.8 60.2 + - + +
964B MET* 4.9 0.4 - - - -
966B THR* 1.3 86.6 - - - +
968B LEU* 1.3 67.0 + - + +
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Residues in contact with LEU 968 (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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51B LYS 3.6 24.7 - - - +
52B ASN* 3.7 10.5 - - + +
55B ILE* 4.0 9.6 - - + -
56B THR* 3.5 31.9 - - + -
964B MET* 2.9 36.8 + - + +
967B GLN* 1.3 88.8 - - + +
969B GLY* 1.3 64.8 + - - +
970B TRP* 3.3 26.6 + - + +
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Residues in contact with GLY 969 (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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965B LYS* 2.8 25.6 + - - +
966B THR 4.4 1.0 + - - -
968B LEU* 1.3 78.8 - - - +
970B TRP* 1.3 63.5 + - - +
971B PRO* 3.4 9.0 - - - +
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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