Contacts of the helix formed by residues 927 - 941 (chain B) in PDB entry 5MQF
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 PRO 927 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908B PRO* 4.1 21.1 - - + -
909B GLY* 4.1 30.1 - - - +
910B ASP 4.8 7.1 - - - +
916B ILE* 5.3 0.4 - - - -
926B ALA* 1.3 86.3 - - + +
928B HIS* 1.3 57.6 + - - +
929B LEU 3.0 0.9 - - - -
930B ALA* 2.8 20.1 + - + +
931B ARG* 2.9 14.3 + - + +
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Residues in contact with HIS 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915B SER 5.1 0.9 - - - +
916B ILE* 3.1 46.2 - - - +
918B ILE* 6.0 1.3 - - + -
924B GLN* 3.7 17.5 - - + -
926B ALA* 2.9 7.2 + - + +
927B PRO* 1.3 78.1 - - - +
929B LEU* 1.3 56.1 + - - +
932B GLU* 2.8 32.7 + - - +
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Residues in contact with LEU 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B PRO* 6.3 1.1 - - + -
924B GLN* 3.3 36.2 - - + +
926B ALA 3.1 6.4 + - - +
927B PRO 3.0 0.8 - - - -
928B HIS* 1.3 78.2 - - - +
930B ALA* 1.3 57.2 + - - +
932B GLU* 3.8 4.1 - - - +
933B PHE* 2.9 27.0 + - - +
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Residues in contact with ALA 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B LEU* 5.7 6.3 - - + -
907B VAL* 4.7 7.2 - - + -
908B PRO* 4.6 21.3 - - + +
909B GLY 4.6 12.8 - - - +
910B ASP 6.0 0.2 - - - -
911B PRO* 5.1 5.1 - - + +
927B PRO* 2.8 13.6 + - + +
929B LEU* 1.3 77.2 - - - +
931B ARG* 1.3 59.3 + - - +
933B PHE* 3.0 8.6 + - - +
934B MET* 2.9 27.2 + - - +
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Residues in contact with ARG 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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910B ASP 4.8 1.5 + - - +
911B PRO* 4.0 29.9 - - + +
912B LEU* 4.0 8.5 + - - +
913B ASP* 4.4 8.5 - - + +
916B ILE* 3.7 25.4 - - + -
927B PRO 2.9 11.8 + - - +
928B HIS* 4.6 0.2 - - - -
930B ALA* 1.3 76.1 - - - +
932B GLU* 1.3 58.0 + - - +
934B MET* 3.2 3.0 + - - +
935B ILE* 2.9 29.1 + - - +
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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
----------------------------------------------------------
916B ILE* 4.9 6.2 - - + +
917B VAL* 6.0 2.9 - - - -
928B HIS 2.8 22.6 + - - +
929B LEU* 3.9 5.4 - - - +
931B ARG* 1.3 76.2 - - - +
933B PHE* 1.3 58.5 + - - +
935B ILE* 4.2 6.0 - - - +
936B LYS* 2.9 32.9 + - - +
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Residues in contact with PHE 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 6.2 6.5 - - + +
929B LEU 2.9 19.2 + - - +
930B ALA* 3.0 11.4 + - - +
932B GLU* 1.3 77.2 - - - +
934B MET* 1.3 49.4 + - - +
936B LYS* 4.5 3.5 - - - +
937B THR* 2.7 36.6 + - - -
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Residues in contact with MET 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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779B LEU* 5.6 6.0 - - + +
780B CYS* 5.2 16.8 - - + +
911B PRO* 4.2 21.5 - - + -
912B LEU 5.7 0.4 - - - +
930B ALA 2.9 11.5 + - - +
931B ARG 3.6 7.4 - - - +
933B PHE* 1.3 76.9 - - - +
935B ILE* 1.3 59.4 + - - +
937B THR* 3.5 5.8 - - - -
938B ARG* 2.9 28.9 + - - +
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Residues in contact with ILE 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 ARG 2.9 17.1 + - - +
932B GLU* 4.2 5.6 - - - +
934B MET* 1.3 76.4 - - - +
936B LYS* 1.3 57.1 + - - +
938B ARG* 3.2 6.9 + - - +
939B ARG* 2.9 28.2 + - - +
945B GLU* 5.7 11.6 - - + +
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Residues in contact with LYS 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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301A LYS* 3.8 32.7 - - + +
302A ILE* 4.4 13.0 - - - +
303A ILE 5.2 0.4 - - - +
932B GLU 2.9 20.2 + - - +
933B PHE* 4.5 2.7 - - - +
935B ILE* 1.3 77.5 - - - +
937B THR* 1.3 56.5 + - - +
939B ARG* 4.0 7.5 - - - +
940B ARG* 2.9 32.6 + - - +
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Residues in contact with THR 937 (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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662B PHE* 5.7 8.1 - - - -
780B CYS* 5.0 14.6 - - - -
933B PHE 2.7 24.9 + - - -
934B MET* 3.5 8.5 - - - -
935B ILE 3.2 0.2 - - - -
936B LYS* 1.3 79.6 - - - +
938B ARG* 1.3 50.0 + - - +
940B ARG* 4.4 2.2 - - - +
941B LYS* 2.7 39.0 + - - +
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Residues in contact with ARG 938 (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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779B LEU 5.0 9.4 - - - +
780B CYS* 6.0 2.4 - - - +
934B MET 2.9 17.4 + - - +
935B ILE* 3.7 6.3 - - - +
937B THR* 1.3 75.7 - - - +
939B ARG* 1.3 58.7 + - - +
941B LYS* 4.3 1.8 - - - -
942B GLY 2.9 7.3 + - - -
943B LEU* 2.5 54.3 + - + +
944B SER 3.7 14.8 - - - +
945B GLU* 5.1 4.7 - - - +
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Residues in contact with ARG 939 (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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301A LYS* 5.4 9.9 - - + +
935B ILE 2.9 16.3 + - - +
936B LYS* 4.0 7.6 - - - +
938B ARG* 1.3 77.0 - - - +
940B ARG* 1.3 61.5 + - - +
942B GLY* 3.4 10.9 + - - -
943B LEU 3.8 5.8 + - - -
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Residues in contact with ARG 940 (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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299A ILE* 5.5 7.6 - - + -
301A LYS 5.4 5.6 + - - +
302A ILE* 6.5 0.2 - - - -
624B SER* 4.6 8.3 - - - -
936B LYS 2.9 19.2 + - - +
937B THR* 4.4 2.7 - - - +
939B ARG* 1.3 77.2 - - - +
941B LYS* 1.3 59.5 + - - +
942B GLY 3.2 1.4 + - - -
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Residues in contact with LYS 941 (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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622B GLU* 5.3 6.3 - - - +
623B GLU* 4.4 10.2 + - - +
624B SER* 4.1 17.1 + - - -
780B CYS 5.7 4.9 - - - +
781B ASP* 6.4 1.8 - - + -
937B THR 2.7 24.0 + - - +
938B ARG* 4.0 4.7 - - - +
939B ARG 3.3 0.2 - - - -
940B ARG* 1.3 76.0 - - - +
942B GLY* 1.3 60.8 + - - +
943B LEU* 3.5 4.8 - - + +
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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