Contacts of the helix formed by residues 996 - 1004 (chain B) in PDB entry 5M64
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 PHE 996 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706B PHE* 4.0 11.7 - + - -
964B VAL* 4.4 4.3 - - + -
967B LEU* 4.5 20.6 - - + +
968B ALA* 3.5 33.2 - - + -
971B ALA* 4.5 3.7 - - + +
977B ILE* 6.3 1.8 - - + -
979B GLN* 4.0 18.8 - - + -
986B PHE* 3.6 33.7 - + - -
992B PRO* 3.0 30.4 + - + +
993B ALA 5.1 0.2 - - - +
995B TYR* 1.3 104.1 - + - +
997B GLY* 1.3 63.3 + - - +
998B GLU 3.3 0.2 - - - -
999B GLN* 3.5 20.0 + - - +
1000B LEU* 3.3 22.9 - - - +
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Residues in contact with GLY 997 (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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967B LEU* 4.8 8.2 - - - +
993B ALA 3.1 23.8 + - - -
994B ASP* 3.4 1.5 + - - -
996B PHE* 1.3 78.2 - - - +
998B GLU* 1.3 58.4 + - - +
1000B LEU* 3.2 5.4 + - - +
1001B ALA* 2.9 29.6 + - - +
1007B TYR* 4.0 24.9 - - - -
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Residues in contact with GLU 998 (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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994B ASP 3.0 16.0 + - - +
995B TYR* 3.2 40.4 - - - +
997B GLY* 1.3 76.1 - - - +
999B GLN* 1.3 60.5 + - + +
1001B ALA* 3.9 7.2 - - - +
1002B LYS* 3.0 30.0 + - - +
1007B TYR* 4.3 8.0 - - + -
162N LYS* 3.8 26.4 + - - +
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Residues in contact with GLN 999 (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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971B ALA* 3.3 27.2 - - + +
974B LEU* 6.0 1.1 - - - -
975B HIS* 4.5 16.5 + - + +
977B ILE* 4.5 16.7 - - - +
995B TYR* 3.8 38.2 + - - +
996B PHE* 3.5 13.0 + - - +
997B GLY 3.2 0.8 - - - -
998B GLU* 1.3 77.7 - - + +
1000B LEU* 1.3 58.7 + - - +
1002B LYS* 3.6 4.4 + - - +
1003B ALA* 3.0 29.3 + - - +
162N LYS* 4.3 17.6 - - - +
163N VAL* 3.9 23.8 - - - +
166N LEU* 4.9 7.4 - - + -
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Residues in contact with LEU1000 (chain B).
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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967B LEU* 3.9 13.5 - - + -
970B LYS* 3.7 24.2 - - + -
971B ALA* 3.7 31.6 - - + +
974B LEU* 5.5 4.9 - - + -
996B PHE 3.3 17.3 - - - +
997B GLY* 3.2 6.4 + - - +
999B GLN* 1.3 76.1 - - - +
1001B ALA* 1.3 64.3 + - - +
1003B ALA* 3.2 4.7 + - - -
1004B GLY 3.0 5.5 + - - -
1005B TYR* 2.8 53.7 + - + -
1006B ASN 3.8 7.2 - - - +
1009B GLY* 3.7 29.6 - - - +
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Residues in contact with ALA1001 (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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997B GLY 2.9 17.5 + - - +
998B GLU* 3.9 6.7 - - - +
1000B LEU* 1.3 79.2 - - - +
1002B LYS* 1.3 58.6 + - - +
1004B GLY* 3.5 8.0 + - - -
1005B TYR 3.2 12.2 + - - +
1006B ASN 4.3 0.4 + - - -
1007B TYR* 4.1 12.1 - - + -
250C CYS 5.7 0.5 - - - +
278C GLU* 3.8 30.0 - - - +
281C ARG* 4.6 4.0 - - - +
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Residues in contact with LYS1002 (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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975B HIS* 5.0 4.5 - - + -
998B GLU 3.0 19.8 + - - +
999B GLN* 4.0 5.8 - - - +
1001B ALA* 1.3 77.2 - - - +
1003B ALA* 1.3 61.6 + - - +
1004B GLY 3.5 1.0 + - - -
166N LEU* 2.8 50.7 + - + +
167N LYS* 3.9 5.7 - - - +
168N LEU* 3.6 32.4 - - + +
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Residues in contact with ALA1003 (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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974B LEU* 3.6 30.5 - - + -
975B HIS* 4.0 12.8 - - + +
999B GLN 3.0 18.7 + - - +
1000B LEU* 3.2 6.2 + - - +
1002B LYS* 1.3 76.7 - - - +
1004B GLY* 1.3 56.0 + - - +
1005B TYR* 3.6 3.6 - - + +
168N LEU* 3.7 20.3 - - + +
169N GLU 3.7 6.9 - - - +
170N HIS* 3.7 21.1 + - - +
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Residues in contact with GLY1004 (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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1000B LEU 3.0 2.0 + - - -
1001B ALA 3.5 5.7 + - - -
1002B LYS 3.3 4.6 + - - -
1003B ALA* 1.3 77.7 - - - +
1005B TYR* 1.3 65.8 + - - +
274C THR* 4.7 1.9 - - - +
276C SER* 3.3 14.9 + - - -
170N HIS* 3.2 28.9 + - - -
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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