Contacts of the helix formed by residues 926 - 936 (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 THR 926 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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904B ILE* 3.7 2.5 - - - +
905B ALA 3.3 4.7 - - - +
906B SER* 4.4 6.3 - - - +
925B VAL* 1.3 82.0 - - - +
927B PRO* 1.3 75.5 - - + +
928B GLU* 3.3 31.8 + - - +
929B TRP* 3.0 20.3 + - - +
930B LEU 4.0 0.7 + - - -
945B TYR* 3.3 16.2 + - - +
946B ILE 5.2 0.7 - - - +
947B LEU* 3.7 29.8 - - + -
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Residues in contact with PRO 927 (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* 4.2 9.6 - - + -
882B TYR* 3.4 40.6 - - + +
904B ILE* 3.4 20.8 - - + -
905B ALA 3.8 14.8 - - - +
906B SER* 4.1 10.1 - - - +
926B THR* 1.3 90.7 - - - +
928B GLU* 1.3 57.0 + - + +
930B LEU* 2.7 29.8 + - + +
931B GLU* 2.8 17.4 + - + +
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Residues in contact with GLU 928 (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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926B THR* 3.0 21.3 + - - +
927B PRO* 1.3 83.8 - - + +
929B TRP* 1.3 61.1 + - - +
931B GLU* 3.8 9.9 - - + +
932B GLU* 3.0 25.8 + - - +
945B TYR* 4.1 14.4 - - + -
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Residues in contact with TRP 929 (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* 4.8 4.0 - - + -
869B VAL* 5.1 4.7 - - + -
902B HIS* 3.5 28.7 - + + -
904B ILE* 4.3 15.7 - - + -
925B VAL* 3.7 22.4 - - + -
926B THR* 3.0 13.9 + - - +
928B GLU* 1.3 77.7 - - - +
930B LEU* 1.3 74.8 + - + +
932B GLU 3.4 0.3 + - - -
933B CYS* 2.9 48.3 + - - -
939B PHE* 3.5 33.0 - + + -
940B ILE* 2.9 32.6 + - + +
942B GLU* 3.6 29.3 - - + +
945B TYR* 3.5 44.4 - + + -
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Residues in contact with LEU 930 (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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871B PHE* 4.3 12.8 - - + -
882B TYR* 3.5 51.8 - - + +
885B LYS* 4.8 7.2 - - + -
886B LEU* 4.4 20.2 - - + +
889B LEU* 4.0 22.2 - - + -
904B ILE* 4.4 14.6 - - + -
926B THR 4.0 0.2 + - - -
927B PRO* 2.7 18.0 + - + +
929B TRP* 1.3 79.9 - - + +
931B GLU* 1.3 57.9 + - + +
932B GLU 2.9 4.0 - - - -
933B CYS* 2.8 19.9 + - - +
934B PHE* 2.9 13.3 + - - +
939B PHE* 4.6 10.8 - - + -
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Residues in contact with GLU 931 (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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882B TYR* 3.5 29.3 - - + -
885B LYS* 3.1 31.0 + - + +
927B PRO* 2.8 26.2 + - + +
928B GLU* 4.0 9.2 - - + +
930B LEU* 1.3 71.6 - - + +
932B GLU* 1.3 57.4 + - - +
934B PHE* 4.0 8.3 - - - +
935B ARG* 3.2 42.9 + - - +
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Residues in contact with GLU 932 (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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928B GLU 3.0 18.2 + - - +
929B TRP 3.7 0.2 - - - +
930B LEU 2.9 0.4 - - - -
931B GLU* 1.3 77.7 - - - +
933B CYS* 1.3 64.0 + - - +
934B PHE 3.1 1.6 - - - -
935B ARG* 3.2 33.4 + - - +
936B CYS* 3.0 44.3 + - - +
940B ILE* 3.2 15.7 - - + -
945B TYR* 3.0 29.4 - - + +
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Residues in contact with CYS 933 (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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889B LEU* 3.3 16.9 - - + +
929B TRP* 2.9 52.9 + - - -
930B LEU* 2.8 9.7 + - - +
932B GLU* 1.3 75.8 - - - +
934B PHE* 1.3 57.6 + - - +
937B GLN 3.0 4.5 + - - -
938B LYS 2.7 42.3 + - - +
939B PHE* 3.6 10.1 - - + -
940B ILE* 3.3 29.3 - - - +
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Residues in contact with PHE 934 (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* 3.5 55.0 - - + +
888B ILE* 3.5 43.3 - - + -
889B LEU* 3.7 14.3 - - + +
930B LEU 2.9 13.0 + - - +
931B GLU 4.0 6.3 - - - +
932B GLU 3.1 0.2 - - - -
933B CYS* 1.3 75.8 - - - +
935B ARG* 1.3 62.2 + - + +
937B GLN* 2.8 28.6 + - - +
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Residues in contact with ARG 935 (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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931B GLU* 3.2 26.2 + - - +
932B GLU* 3.2 32.2 + - - +
934B PHE* 1.3 82.5 - - + +
936B CYS* 1.3 58.8 + - - +
937B GLN* 3.2 11.1 + - - +
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Residues in contact with CYS 936 (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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932B GLU* 3.0 37.9 + - - +
933B CYS 4.0 1.8 - - - +
935B ARG* 1.3 73.6 - - - +
937B GLN* 1.3 70.4 + - - +
938B LYS* 2.8 13.7 + - + +
940B ILE* 3.7 26.5 - - + -
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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