Contacts of the helix formed by residues 997 - 1009 (chain A) in PDB entry 5AMN
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 VAL 997 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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931A GLN* 3.9 24.0 - - - +
995A ARG 4.8 2.7 - - - +
996A PRO* 1.3 77.5 - - - +
998A PHE* 1.3 60.0 + - - +
999A ALA* 3.9 10.8 - - + +
1000A ASP* 2.8 44.0 + - - +
1001A ILE* 3.1 11.5 + - - +
2015A FMT 3.3 21.1 - - - +
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Residues in contact with PHE 998 (chain A).
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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859A SER* 3.3 13.4 + - - +
862A MET* 3.5 57.7 - - + -
863A GLN* 4.0 17.7 - - + +
875A LEU* 4.4 0.2 - - + -
930A THR* 3.9 20.9 - - + -
933A ASP* 3.9 23.3 - - + -
934A VAL* 3.8 14.4 - - + -
937A PHE* 3.9 24.7 - + + -
997A VAL* 1.3 74.2 - - - +
999A ALA* 1.3 61.0 + - - +
1001A ILE* 3.7 17.5 - - + +
1002A SER* 3.1 27.5 + - - -
2015A FMT 3.4 19.7 + - - +
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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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863A GLN* 3.5 28.4 + - - +
997A VAL* 3.0 9.5 + - + -
998A PHE* 1.3 77.7 - - - +
1000A ASP* 1.3 63.5 + - - +
1002A SER* 3.7 2.9 + - - -
1003A LYS* 3.2 22.0 + - - +
2015A FMT 3.2 15.5 + - - +
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Residues in contact with ASP1000 (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 PRO* 3.9 16.9 - - + +
997A VAL* 2.8 35.5 + - - +
999A ALA* 1.3 78.6 - - - +
1001A ILE* 1.3 54.9 + - - +
1003A LYS* 3.3 6.8 + - - +
1004A ASP* 2.7 43.2 + - - +
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Residues in contact with ILE1001 (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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859A SER* 3.4 13.0 - - - +
934A VAL* 4.2 13.5 - - + -
937A PHE* 3.5 37.5 - - + -
983A LEU* 4.3 12.3 - - + -
987A CYS* 4.2 13.7 - - - -
996A PRO* 4.2 14.4 - - + -
997A VAL 3.1 9.3 + - - +
998A PHE* 3.6 33.2 - - + +
999A ALA 3.3 0.2 - - - -
1000A ASP* 1.3 73.2 - - - +
1002A SER* 1.3 60.4 + - - +
1004A ASP* 3.2 6.9 + - - +
1005A LEU* 2.8 45.9 + - + +
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Residues in contact with SER1002 (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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856A TRP* 3.6 10.6 - - - -
859A SER* 2.7 29.0 + - - -
860A GLN* 3.8 19.6 + - - +
863A GLN* 3.1 23.8 + - - -
998A PHE 3.1 9.0 + - - -
999A ALA 3.8 4.0 - - - -
1001A ILE* 1.3 74.2 - - - +
1003A LYS* 1.3 59.2 + - - +
1005A LEU* 3.2 1.1 + - - -
1006A GLU* 2.9 39.9 + - - +
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Residues in contact with LYS1003 (chain A).
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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999A ALA 3.2 12.8 + - - +
1000A ASP* 3.5 11.4 - - - +
1002A SER* 1.3 78.7 - - - +
1004A ASP* 1.3 65.2 + - - +
1006A GLU* 3.4 12.4 + - - +
1007A LYS* 3.1 23.4 + - - +
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Residues in contact with ASP1004 (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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983A LEU* 3.6 28.5 - - + +
986A GLN* 4.7 9.7 - - - -
996A PRO* 5.5 2.4 - - - +
1000A ASP* 2.7 25.8 + - - +
1001A ILE* 3.5 7.9 - - - +
1003A LYS* 1.3 76.0 - - - +
1005A LEU* 1.3 62.0 + - - +
1007A LYS* 3.2 8.9 + - - +
1008A MET* 3.1 30.6 + - + +
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Residues in contact with LEU1005 (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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852A ILE* 3.7 12.5 - - + +
855A ALA* 3.7 22.0 - - + +
856A TRP* 3.6 39.0 - - + +
859A SER* 4.0 3.4 - - - -
937A PHE* 4.1 2.7 - - + -
941A LEU* 4.7 0.4 - - + -
980A MET* 4.2 13.0 - - + -
983A LEU* 3.8 20.4 - - + -
1001A ILE* 2.8 40.8 + - + +
1002A SER 3.7 3.1 - - - +
1004A ASP* 1.3 72.3 - - - +
1006A GLU* 1.3 61.0 + - - +
1008A MET* 3.3 32.4 + - - +
1009A MET* 3.4 12.4 + - - +
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Residues in contact with GLU1006 (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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856A TRP* 2.8 43.6 + - + +
860A GLN* 3.9 7.3 + - - -
1002A SER* 2.9 25.2 + - - +
1003A LYS* 3.7 9.9 - - - +
1005A LEU* 1.3 73.0 - - - +
1007A LYS* 1.3 65.3 + - - +
1009A MET* 3.1 32.3 + - + +
1010A VAL* 3.5 10.6 + - - +
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Residues in contact with LYS1007 (chain A).
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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1003A LYS 3.1 14.1 + - - +
1004A ASP* 3.2 11.0 + - - +
1006A GLU* 1.3 76.6 - - - +
1008A MET* 1.3 61.6 + - - +
1010A VAL* 3.2 24.2 + - - +
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Residues in contact with MET1008 (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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852A ILE* 4.3 19.4 - - + +
977A SER* 5.3 1.6 - - - -
979A GLU* 3.1 48.9 - - + +
980A MET* 3.4 39.3 - - + +
983A LEU* 4.5 14.4 - - + -
1004A ASP* 3.1 21.2 + - + +
1005A LEU* 3.3 18.2 - - - +
1006A GLU 3.1 0.4 - - - -
1007A LYS* 1.3 78.1 - - + +
1009A MET* 1.3 56.2 + - - +
1010A VAL 3.2 6.0 + - - +
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Residues in contact with MET1009 (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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849A GLY* 6.1 3.8 - - - +
852A ILE* 4.5 17.7 - - + -
853A SER* 5.4 7.2 - - - -
856A TRP* 3.9 27.6 - - + +
1005A LEU 3.5 7.9 - - - +
1006A GLU* 3.1 47.3 + - + +
1008A MET* 1.3 75.5 - - - +
1010A VAL* 1.3 58.7 + - - +
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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