Contacts of the helix formed by residues 875 - 889 (chain B) in PDB entry 3SQD
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 GLU 875 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873B GLY 4.3 0.2 + - - -
874B PHE* 1.3 76.4 - - - +
876B PRO* 1.3 78.0 - - + +
877B VAL* 3.4 6.6 - - + +
878B GLN* 3.1 21.9 + - + +
879B VAL* 3.0 20.5 + - - +
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Residues in contact with PRO 876 (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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874B PHE 3.8 2.0 - - - +
875B GLU* 1.3 88.3 - - + +
877B VAL* 1.3 67.2 + - + +
879B VAL* 3.2 10.7 + - + +
880B GLN* 3.0 31.2 + - - +
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Residues in contact with VAL 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B GLU* 3.4 5.7 - - + +
876B PRO* 1.3 79.3 - - + +
878B GLN* 1.3 64.1 + - - +
880B GLN* 3.0 41.6 + - - +
881B GLN* 3.2 22.5 + - + +
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Residues in contact with GLN 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874B PHE* 3.7 20.8 - - + +
875B GLU* 3.1 32.9 + - + +
877B VAL* 1.3 79.6 - - - +
879B VAL* 1.3 62.8 - - - +
881B GLN* 3.4 26.7 + - - +
882B TYR* 3.3 45.3 + - + +
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Residues in contact with VAL 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B PHE* 4.2 23.1 - - + -
874B PHE* 3.4 33.4 - - + +
875B GLU 3.0 18.6 + - - +
876B PRO* 3.3 10.8 - - + +
877B VAL 3.1 0.2 - - - -
878B GLN* 1.3 74.9 - - - +
880B GLN* 1.3 66.7 + - + +
882B TYR* 3.0 12.8 + - - +
883B ILE* 2.9 39.8 + - + +
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Residues in contact with GLN 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876B PRO* 3.0 22.3 + - - +
877B VAL* 3.0 35.1 + - - +
879B VAL* 1.3 76.7 - - + +
881B GLN* 1.3 61.8 + - + +
883B ILE* 3.1 18.4 + - - +
884B LYS* 3.1 32.2 + - - +
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Residues in contact with GLN 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877B VAL* 3.2 23.9 + - + +
878B GLN* 3.4 27.1 - - - +
879B VAL 3.2 0.8 - - - -
880B GLN* 1.3 76.7 - - + +
882B TYR* 1.3 66.6 + - + +
884B LYS* 3.4 17.1 + - - +
885B LYS* 3.4 25.5 + - - +
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Residues in contact with TYR 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B PHE* 3.6 31.6 - + + -
874B PHE* 3.9 27.2 - + - -
878B GLN* 3.3 41.4 + - + -
879B VAL* 3.0 12.4 + - - +
881B GLN* 1.3 79.6 - - + +
883B ILE* 1.3 58.6 + - - +
885B LYS* 3.3 6.7 + - + +
886B LEU* 2.8 28.0 + - - +
927B PRO* 3.4 33.6 - - + +
930B LEU* 3.5 24.1 - - + +
931B GLU* 3.5 28.3 - - + -
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Residues in contact with ILE 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B PHE* 3.7 20.4 - - + -
879B VAL* 2.9 31.1 + - + +
880B GLN* 3.1 11.0 + - - +
882B TYR* 1.3 74.7 - - - +
884B LYS* 1.3 76.3 + - - +
886B LEU* 3.5 6.0 - - + +
887B TYR* 2.9 55.9 + - + +
893B VAL* 3.5 25.1 - - + -
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Residues in contact with LYS 884 (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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880B GLN* 3.1 29.0 + - - +
881B GLN* 3.8 9.9 - - - +
882B TYR 3.3 0.4 - - - -
883B ILE* 1.3 91.5 - - + +
885B LYS* 1.3 65.2 + - + +
887B TYR* 3.3 14.3 + - + +
888B ILE* 3.0 36.0 + - + +
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Residues in contact with LYS 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881B GLN* 3.4 22.0 - - - +
882B TYR* 3.3 9.6 + - + +
883B ILE 3.2 0.2 - - - -
884B LYS* 1.3 79.6 - - + +
886B LEU* 1.3 62.4 + - - +
888B ILE* 3.4 2.6 + - + +
889B LEU* 3.0 30.3 + - - +
930B LEU* 4.8 9.4 - - + -
931B GLU* 3.1 37.1 + - + +
934B PHE* 3.5 54.1 - - + -
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Residues in contact with LEU 886 (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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867B PRO* 5.0 0.2 - - + -
869B VAL* 3.7 33.7 - - + -
871B PHE* 4.5 8.1 - - + -
882B TYR 2.8 18.3 + - - +
883B ILE* 3.3 6.7 + - - +
885B LYS* 1.3 76.4 - - - +
887B TYR* 1.3 57.5 + - + +
889B LEU* 3.3 4.5 + - - +
890B GLY 3.1 3.8 + - - -
891B GLY* 2.6 57.0 + - - -
892B GLU 3.7 26.5 - - - +
893B VAL* 3.9 16.6 - - + +
929B TRP* 6.1 0.2 - - + -
930B LEU* 4.4 17.1 - - + +
939B PHE* 3.9 16.4 - - + -
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Residues in contact with TYR 887 (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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883B ILE* 2.9 41.6 + - + +
884B LYS* 3.6 16.4 - - + +
886B LEU* 1.3 75.0 - - + +
888B ILE* 1.3 63.1 + - + +
890B GLY* 2.9 19.4 + - - -
891B GLY 3.7 18.8 - - - -
892B GLU* 4.7 1.1 - - - -
893B VAL* 4.1 27.9 - - + +
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Residues in contact with ILE 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884B LYS* 3.0 26.9 + - + +
885B LYS* 3.6 6.3 - - + +
887B TYR* 1.3 75.3 - - + +
889B LEU* 1.3 64.7 + - + +
890B GLY* 3.2 1.4 + - - -
934B PHE* 3.5 36.3 - - + -
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Residues in contact with LEU 889 (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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885B LYS 3.0 20.7 + - - +
886B LEU 3.7 1.1 - - - +
887B TYR 3.2 0.2 - - - -
888B ILE* 1.3 76.2 - - + +
890B GLY* 1.3 59.6 + - - +
891B GLY 3.3 0.2 - - - -
930B LEU* 4.0 17.5 - - + -
933B CYS* 3.3 32.3 - - + +
934B PHE* 3.7 34.5 - - + +
937B GLN* 3.7 12.3 - - - +
938B LYS* 3.6 18.6 - - - +
939B PHE* 3.6 30.4 - - + -
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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