Contacts of the helix formed by residues 996 - 1002 (chain B) in PDB entry 3Q0L
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 GLN 996 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962B LEU* 4.6 15.0 - - + +
966B LYS* 6.1 2.0 - - - -
992B ALA 4.2 11.4 - - - +
993B PHE 2.8 13.1 + - - +
994B LYS 3.9 7.5 + - - +
995B GLY* 1.3 86.8 - - - +
997B VAL* 1.3 55.3 + - - +
998B PHE 3.3 2.9 - - - -
999B ALA* 3.1 17.5 + - + +
1000B LEU* 2.6 57.4 + - + +
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Residues in contact with VAL 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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993B PHE* 3.4 10.0 + - + +
996B GLN* 1.3 76.6 - - - +
998B PHE* 1.3 59.4 + - - +
1000B LEU* 3.6 1.8 - - - +
1001B SER* 2.7 36.9 + - - +
1010B ILE* 4.4 15.6 - - + +
1025B ILE* 3.8 41.5 - - + +
1028B GLU* 3.2 39.0 + - + +
1029B LEU* 3.6 30.3 - - + -
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Residues in contact with PHE 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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995B GLY 5.3 0.8 + - - +
996B GLN 3.3 0.4 - - - -
997B VAL* 1.3 79.2 - - - +
999B ALA* 1.3 71.1 + - - +
1001B SER* 2.9 15.7 + - - -
1002B THR* 3.2 30.9 + - + +
1028B GLU* 4.5 5.1 + - + +
1032B HIS* 3.6 48.5 - + + +
1035B GLN* 3.7 39.9 - - + -
1036B LEU* 3.7 26.0 - - + -
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Residues in contact with ALA 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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995B GLY 5.2 1.7 + - - +
996B GLN* 3.1 28.1 + - + +
998B PHE* 1.3 83.1 - - + +
1000B LEU* 1.3 64.0 + - + +
1002B THR* 3.2 18.1 + - - -
1003B HIS* 3.6 12.0 + - - +
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Residues in contact with LEU1000 (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 LEU* 4.0 6.3 - - + -
965B VAL* 4.0 20.6 - - + -
966B LYS* 4.0 26.9 - - + +
993B PHE* 3.8 42.6 - - + -
996B GLN* 2.6 43.0 + - + +
997B VAL 4.0 2.5 - - - +
999B ALA* 1.3 74.0 - - + +
1001B SER* 1.3 61.9 + - - +
1002B THR 3.2 2.2 - - - -
1003B HIS* 3.2 11.8 + - + -
1006B GLY* 3.0 13.9 - - - +
1007B CYS 2.9 25.3 + - - -
1010B ILE* 4.5 7.4 - - + -
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Residues in contact with SER1001 (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 VAL* 2.7 25.1 + - - +
998B PHE 2.9 4.4 + - - -
1000B LEU* 1.3 73.4 - - - +
1002B THR* 1.3 58.0 + - - +
1003B HIS 3.3 1.3 - - - -
1007B CYS* 3.4 20.6 - - - +
1010B ILE* 3.9 10.6 - - - +
1029B LEU* 3.5 20.6 - - - +
1036B LEU* 3.7 18.8 - - - -
1041B TYR 3.4 0.2 - - - -
1042B GLY* 3.2 21.7 + - - -
1045B VAL* 3.8 16.0 - - - +
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Residues in contact with THR1002 (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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998B PHE* 3.2 28.0 + - + +
999B ALA* 3.2 15.6 + - - -
1000B LEU 3.2 0.2 - - - -
1001B SER* 1.3 75.6 - - - +
1003B HIS* 1.3 58.2 + - - +
1004B PRO* 4.4 0.5 - - - +
1036B LEU* 3.6 24.5 - - + -
1039B ASP* 3.4 35.7 - - + +
1041B TYR* 3.3 17.6 - - - -
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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