Contacts of the helix formed by residues 994 - 1004 (chain A) in PDB entry 2RD0
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 HIS 994 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A LYS* 5.5 4.9 + - - -
596A GLU* 5.0 9.1 + - - +
823A ILE* 3.7 36.6 - - + +
827A GLN* 3.0 26.7 + - + -
990A ALA 3.0 24.7 - - - +
991A ILE 3.1 9.9 + - - +
993A GLN* 1.3 91.7 + - + +
995A ALA* 1.3 61.3 + - - -
996A ASN* 3.5 7.4 - - - -
997A LEU* 3.4 15.6 - - + +
998A PHE* 3.2 20.2 - - + -
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Residues in contact with ALA 995 (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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538A ASP* 5.6 5.4 - - + -
991A ILE 3.8 3.6 - - - -
992A ARG* 3.0 18.1 + - + +
993A GLN 3.4 2.6 + - - -
994A HIS* 1.3 75.5 - - - +
996A ASN* 1.3 69.4 + - - +
998A PHE* 2.8 21.2 + - - +
999A ILE* 3.2 16.8 + - + +
1026A LEU* 3.8 26.6 - - + +
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Residues in contact with ASN 996 (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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537A ARG 5.3 2.0 - - - +
538A ASP* 4.5 8.0 - - - +
539A PRO* 3.8 22.2 - - + +
596A GLU* 3.2 23.8 + - - +
597A GLN* 3.3 15.4 + - - +
993A GLN 4.7 3.3 - - - +
994A HIS* 4.3 4.5 - - - -
995A ALA* 1.3 77.9 + - - +
997A LEU* 1.3 64.1 + - - +
999A ILE* 3.1 13.0 + - - +
1000A ASN* 2.9 33.0 + - - +
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Residues in contact with LEU 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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596A GLU* 3.3 40.4 + - + +
599A MET* 5.9 2.9 - - - -
631A TYR* 4.6 16.4 - - + +
819A ILE* 3.7 29.8 - - + -
823A ILE* 4.4 7.9 - - + -
994A HIS* 3.4 12.8 - - + +
996A ASN* 1.3 83.0 + - - +
998A PHE* 1.3 68.0 + - + +
1000A ASN* 3.4 10.7 + - + +
1001A LEU* 2.9 47.9 + - + +
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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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816A ILE* 3.7 34.8 - - + -
819A ILE* 3.4 34.5 - - + -
820A MET* 3.8 20.0 - - + -
823A ILE* 3.7 17.7 - - + -
911A LEU* 5.9 0.4 - - + -
991A ILE* 3.6 26.2 - - + -
994A HIS* 3.2 29.8 - - + -
995A ALA* 2.8 13.3 + - - +
997A LEU* 1.3 75.3 - - + +
999A ILE* 1.3 66.0 + - - +
1001A LEU* 3.9 8.0 - - + +
1002A PHE* 2.9 37.1 + - + -
1022A ILE* 4.4 18.8 - - + -
1026A LEU* 5.6 1.6 - - + -
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Residues in contact with ILE 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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538A ASP* 4.4 12.3 - - + -
539A PRO* 4.2 20.4 - - + -
540A LEU* 3.4 38.8 - - + +
995A ALA* 3.2 21.0 + - + +
996A ASN* 3.3 12.8 - - - +
998A PHE* 1.3 77.3 - - - +
1000A ASN* 1.3 50.3 + - - +
1002A PHE* 3.3 2.9 + - - +
1003A SER* 2.4 45.7 + - - +
1016A PHE* 5.8 0.9 - - + -
1019A ILE* 4.0 13.1 - - + +
1022A ILE* 4.3 21.1 - - + -
1023A ARG* 4.6 11.0 - - + -
1026A LEU* 5.4 1.6 - - + -
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Residues in contact with ASN1000 (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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539A PRO* 3.5 12.4 - - - +
596A GLU* 3.4 27.0 + - - +
597A GLN* 4.7 1.8 - - - +
599A MET* 5.3 1.3 - - + -
600A GLU* 3.3 39.4 + - - +
603A ASP* 6.1 0.2 - - - -
996A ASN* 2.9 28.8 + - - +
997A LEU* 3.4 10.6 - - + +
999A ILE* 1.3 74.3 - - - +
1001A LEU* 1.3 53.1 + - + +
1003A SER* 2.6 30.5 + - - -
1004A MET* 2.6 32.9 + - + +
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Residues in contact with LEU1001 (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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599A MET* 4.8 10.1 - - - -
631A TYR* 3.9 21.3 - - + -
634A GLN* 3.4 52.5 + - + +
812A LEU* 5.5 1.1 - - - -
815A GLN* 5.1 1.1 - - - +
816A ILE* 4.9 11.9 - - + -
819A ILE* 4.4 21.8 - - + -
997A LEU* 2.9 51.2 + - + +
998A PHE* 3.9 14.6 - - + +
1000A ASN* 1.3 73.6 - - + +
1002A PHE* 1.3 62.9 + - - +
1004A MET* 3.5 3.5 + - - -
1005A MET* 3.4 15.8 - - - +
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Residues in contact with PHE1002 (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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812A LEU* 4.2 5.2 - - + -
813A THR* 6.5 0.2 - - - -
816A ILE* 3.3 31.4 - - + -
911A LEU* 3.5 27.6 - - + -
937A PHE* 3.0 45.1 - + - -
938A LEU* 4.1 12.3 - - + -
998A PHE* 2.9 34.8 + - + +
999A ILE 3.5 4.3 - - - +
1001A LEU* 1.3 78.7 - - - +
1003A SER* 1.3 57.5 + - - +
1005A MET* 3.0 28.0 + - - +
1006A LEU* 3.7 1.2 + - - +
1013A LEU* 3.7 20.9 - - + +
1019A ILE* 3.8 23.1 - - + -
1022A ILE* 4.7 11.2 - - + -
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Residues in contact with SER1003 (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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539A PRO* 6.0 0.7 - - - +
603A ASP* 4.1 16.4 - - - +
604A CYS* 5.5 0.5 - - - -
641A TYR* 3.8 3.1 + - - -
999A ILE* 2.4 26.2 + - - +
1000A ASN* 2.6 17.8 + - - -
1002A PHE* 1.3 67.3 - - - +
1004A MET* 1.3 56.0 + - - -
1005A MET 2.8 10.1 + - - -
1006A LEU* 3.2 23.3 + - - +
1016A PHE* 3.6 25.8 - - - -
1019A ILE* 3.1 21.9 - - - +
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Residues in contact with MET1004 (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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599A MET* 3.6 55.0 - - + +
600A GLU* 5.7 0.9 - - - -
602A LEU* 5.4 0.9 - - + -
603A ASP* 4.4 9.6 - - + -
634A GLN* 3.0 45.9 - - + +
635A LEU* 3.9 12.8 - - + +
637A GLN* 3.5 20.4 - - - +
638A VAL* 3.9 24.5 - - + +
641A TYR* 3.9 7.0 + - - -
1000A ASN* 2.6 33.5 + - + +
1001A LEU* 3.9 5.2 - - - +
1002A PHE 3.3 0.2 - - - -
1003A SER* 1.3 72.0 - - - +
1005A MET* 1.3 55.9 + - - +
1006A LEU 3.4 2.1 + - - -
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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