Contacts of the strand formed by residues 1009 - 1015 (chain A) in PDB entry 1M7N
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 MET1009 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A GLU* 3.1 29.4 - - + +
1002A LEU 3.3 5.6 - - - +
1003A GLY* 2.8 47.6 - - - +
1004A GLN* 3.3 28.1 - - - +
1008A GLY* 1.3 70.7 - - - -
1010A VAL* 1.3 76.9 + - - +
1011A TYR* 3.2 37.0 - - + +
1031A THR* 2.7 41.4 + - - +
1033A ASN* 4.1 2.9 - - - +
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Residues in contact with VAL1010 (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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1002A LEU* 3.2 23.3 + - + -
1003A GLY 3.7 15.9 + - - +
1005A GLY* 4.2 9.9 - - - -
1008A GLY 3.9 9.0 - - - +
1009A MET* 1.3 101.7 - - - +
1011A TYR* 1.3 75.9 + - - +
1028A ALA* 4.7 3.1 - - + -
1029A ILE 3.3 11.2 - - - +
1030A LYS* 4.1 21.3 - - + +
1152A GLY 4.8 1.8 - - - +
1153A MET* 4.0 31.0 - - + -
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Residues in contact with TYR1011 (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 MET* 3.5 46.9 - - + -
1000A ARG* 3.4 23.8 - - - +
1001A GLU* 3.8 23.1 + - + -
1002A LEU* 3.2 13.1 - - - +
1009A MET* 3.2 36.0 - - + +
1010A VAL* 1.3 77.0 - - - +
1012A GLU* 1.3 62.9 + - - +
1028A ALA* 3.1 7.8 - - - +
1029A ILE* 2.6 46.5 + - + +
1031A THR* 3.9 9.2 - - + -
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Residues in contact with GLU1012 (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 MET* 3.6 3.3 - - - -
999A SER* 2.6 40.1 + - - -
1000A ARG* 3.1 50.1 + - + +
1002A LEU* 3.9 21.0 - - + +
1011A TYR* 1.3 76.0 - - - +
1013A GLY* 1.3 56.9 + - - +
1026A ARG* 3.2 30.2 + - - +
1027A VAL 3.2 5.2 - - - +
1029A ILE* 4.6 2.2 - - - -
1078A LEU* 3.7 22.4 - - + +
1080A THR* 5.4 2.6 - - - +
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Residues in contact with GLY1013 (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 THR 3.2 13.7 - - - -
999A SER* 3.5 13.0 - - - -
1012A GLU* 1.3 80.5 - - - +
1014A VAL* 1.3 67.2 + - - +
1026A ARG* 3.2 9.5 - - - +
1027A VAL* 2.8 36.1 + - - -
1029A ILE* 4.4 3.0 - - - +
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Residues in contact with VAL1014 (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 LYS 4.0 0.6 - - - +
996A ILE* 3.5 4.0 - - - +
997A THR* 3.0 44.1 + - - +
999A SER* 4.9 5.6 - - - +
1013A GLY* 1.3 80.8 - - - +
1015A ALA* 1.3 68.8 + - - +
1016A LYS* 5.6 1.3 - - + -
1024A GLU* 3.4 46.4 - - + +
1025A THR 3.1 10.8 - - - +
1026A ARG* 4.7 10.8 - - + -
1027A VAL* 4.0 1.8 - - - -
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Residues in contact with ALA1015 (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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991A VAL* 5.9 0.4 - - + -
995A LYS* 3.2 9.2 - - + +
996A ILE* 4.2 15.3 - - + -
1014A VAL* 1.3 78.6 - - - +
1016A LYS* 1.3 60.3 + - - +
1018A VAL* 2.7 37.6 - - + +
1024A GLU 4.0 0.2 - - - -
1025A THR 3.0 20.6 + - - -
1027A VAL* 4.0 18.6 - - + -
1075A ILE* 4.2 11.0 - - + -
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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