Contacts of the helix formed by residues 996 - 1002 (chain A) in PDB entry 1M8X
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A LEU* 4.9 14.6 - - + +
966A LYS* 5.5 4.3 + - - -
992A ALA 4.7 7.0 - - - +
993A PHE 2.8 11.7 + - - +
994A LYS 4.6 4.3 - - - +
995A GLY* 1.3 95.1 + - - +
997A VAL* 1.3 60.4 + - - +
998A PHE* 3.3 2.2 - - - -
999A ALA* 3.2 23.2 + - + +
1000A LEU* 2.8 45.5 + - + +
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Residues in contact with VAL 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993A PHE* 3.6 14.6 - - + +
994A LYS* 5.1 0.2 - - - -
996A GLN* 1.3 74.8 - - - +
998A PHE* 1.3 62.8 + - - +
1000A LEU* 4.1 4.7 - - - +
1001A SER* 2.8 46.5 + - - +
1010A ILE* 4.4 6.5 - - + -
1025A ILE* 3.9 45.3 - - + +
1028A GLU* 3.1 34.8 + - + +
1029A LEU* 3.8 20.9 - - + +
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Residues in contact with PHE 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A GLY 6.0 0.7 - - - +
996A GLN* 3.3 0.8 - - - +
997A VAL* 1.3 84.4 - - - +
999A ALA* 1.3 65.6 + - - +
1001A SER* 3.2 9.2 + - - -
1002A THR* 3.4 25.2 + - + +
1028A GLU* 4.2 4.9 + - - +
1032A HIS* 3.5 48.7 - + + +
1035A GLN* 3.5 46.9 - - + -
1036A LEU* 3.6 29.4 - - + -
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Residues in contact with ALA 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996A GLN* 3.2 35.4 + - + +
998A PHE* 1.3 84.1 - - + +
1000A LEU* 1.3 63.4 + - + +
1002A THR* 3.2 18.5 + - - -
1003A HIS* 3.4 10.9 + - - +
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Residues in contact with LEU1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962A LEU* 4.1 23.3 - - + -
965A VAL* 4.2 18.2 - - + -
966A LYS* 4.3 19.5 - - + -
993A PHE* 3.2 57.2 - - + -
996A GLN* 2.8 30.7 + - + +
997A VAL 4.1 1.8 - - - +
999A ALA* 1.3 74.5 - - + +
1001A SER* 1.3 64.2 + - - +
1003A HIS* 3.2 13.3 + - + -
1006A GLY* 3.1 10.1 - - - -
1007A CYS 3.1 20.4 + - - -
1010A ILE* 4.6 4.0 - - + -
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Residues in contact with SER1001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A VAL* 2.8 26.6 + - - +
998A PHE 3.2 4.6 + - - -
1000A LEU* 1.3 73.1 - - - +
1002A THR* 1.3 58.1 + - - +
1003A HIS 3.3 0.9 - - - -
1007A CYS* 3.4 22.2 - - - +
1010A ILE* 3.7 16.6 - - - +
1029A LEU* 3.5 22.9 - - - +
1036A LEU* 3.8 18.4 - - - -
1041A TYR 3.6 0.3 - - - -
1042A GLY* 3.3 19.5 + - - -
1045A VAL* 4.1 8.1 - - - +
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Residues in contact with THR1002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998A PHE* 3.4 26.7 + - + +
999A ALA* 3.2 14.7 + - - -
1000A LEU 3.2 0.2 - - - -
1001A SER* 1.3 75.4 - - - +
1003A HIS* 1.3 62.1 + - - +
1004A PRO* 3.9 1.2 - - - +
1036A LEU* 3.8 19.1 - - + -
1039A ASP* 3.2 38.6 - - + +
1041A TYR* 3.5 16.6 - - - -
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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