Contacts of the helix formed by residues 987 - 998 (chain A) in PDB entry 3SQD
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 SER 987 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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984A ILE 4.0 6.1 - - - -
986A PRO* 1.3 80.6 - - - +
988A LEU* 1.3 64.9 + - - +
989A SER* 3.6 10.2 + - - -
990A THR* 3.0 29.0 + - - -
991A MET* 2.9 19.2 + - - +
142C TYR* 5.7 0.4 + - - -
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Residues in contact with LEU 988 (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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980A ILE* 3.7 47.3 - - + +
981A THR 4.5 0.9 - - - +
982A PRO* 4.7 22.3 + - + +
984A ILE* 3.7 14.5 + - + +
987A SER* 1.3 72.3 - - - +
989A SER* 1.3 57.4 + - - +
991A MET* 3.3 1.2 + - - +
992A LYS* 2.9 34.8 + - + +
1002A VAL* 4.9 11.4 - - + -
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Residues in contact with SER 989 (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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987A SER* 3.1 9.5 + - - -
988A LEU* 1.3 80.0 - - - +
990A THR* 1.3 56.8 + - - +
992A LYS* 3.5 9.3 + - - +
993A ALA* 3.1 27.7 + - - +
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Residues in contact with THR 990 (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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912A VAL* 3.8 33.7 - - + +
986A PRO* 3.9 27.2 - - + +
987A SER* 3.0 21.9 + - - -
989A SER* 1.3 76.8 - - - +
991A MET* 1.3 65.6 + - - +
993A ALA* 3.2 6.6 + - - +
994A ILE* 3.0 40.6 + - + +
142C TYR* 4.7 6.4 + - + -
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Residues in contact with MET 991 (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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980A ILE* 3.9 18.8 - - + -
984A ILE* 4.1 12.8 - - + -
986A PRO* 3.6 34.8 - - + +
987A SER 2.9 17.4 + - - +
988A LEU* 3.7 7.2 - - - +
990A THR* 1.3 74.8 - - - +
992A LYS* 1.3 52.8 + - - +
994A ILE* 3.1 6.8 + - - +
995A VAL* 2.7 41.0 + - - +
1027A ILE* 4.3 11.2 - - + -
1049A ALA* 3.8 26.7 - - + +
1052A VAL* 3.7 35.0 - - + -
1053A LEU* 4.3 11.7 - - - -
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Residues in contact with LYS 992 (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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980A ILE* 5.0 0.2 - - - +
988A LEU* 2.9 21.9 + - + +
989A SER* 3.6 9.6 - - - +
991A MET* 1.3 74.6 - - - +
993A ALA* 1.3 60.8 + - - +
995A VAL* 3.8 0.5 - - - +
996A GLU* 2.9 63.3 + - - +
1002A VAL* 3.8 40.1 + - + +
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Residues in contact with ALA 993 (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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912A VAL* 5.1 5.2 - - + -
916A THR* 3.8 14.8 - - + -
989A SER 3.1 17.3 + - - +
990A THR* 3.2 5.6 + - - +
992A LYS* 1.3 77.8 - - - +
994A ILE* 1.3 62.6 + - - +
996A GLU* 4.2 6.4 - - - +
997A CYS* 3.2 31.0 + - - -
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Residues in contact with ILE 994 (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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912A VAL* 4.8 5.2 - - + -
915A LEU* 3.7 36.2 - - + +
916A THR* 3.9 19.1 - - + -
919A SER* 5.0 0.2 + - - -
986A PRO* 5.3 0.2 - - + -
990A THR* 3.0 32.8 + - + +
991A MET* 3.5 8.3 - - - +
993A ALA* 1.3 76.6 - - - +
995A VAL* 1.3 67.5 + - - +
996A GLU 3.4 0.2 + - - -
997A CYS* 3.6 2.6 + - - +
998A ALA* 3.4 19.2 + - - +
1052A VAL* 3.7 22.0 - - + +
1053A LEU* 3.7 27.4 - - + -
1056A VAL* 3.8 14.1 - - + +
142C TYR* 6.3 0.7 - - + -
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Residues in contact with VAL 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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973A PHE* 3.8 8.4 - - + -
978A PHE* 3.6 32.3 - - + -
980A ILE* 4.4 5.4 - - + -
991A MET 2.7 25.9 + - - +
992A LYS 3.8 3.6 - - - +
994A ILE* 1.3 73.4 - - - +
996A GLU* 1.3 60.6 + - - +
998A ALA* 3.2 10.2 + - - +
999A GLY 3.3 0.2 + - - -
1000A GLY* 3.0 43.7 + - - -
1001A LYS 3.9 1.6 - - - +
1002A VAL* 3.9 19.1 - - + -
1052A VAL* 4.1 28.3 - - + -
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Residues in contact with GLU 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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898A GLN* 5.0 13.4 + - - +
992A LYS* 2.9 51.4 + - + +
993A ALA* 4.2 6.0 - - - +
995A VAL* 1.3 75.9 - - + +
997A CYS* 1.3 56.0 + - - +
998A ALA 3.0 4.9 - - - -
999A GLY* 2.7 24.6 + - - -
1000A GLY 3.5 18.9 - - - +
1001A LYS* 4.8 12.9 + - + +
1002A VAL* 4.8 6.1 + - + -
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Residues in contact with CYS 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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897A ALA* 4.2 7.0 - - - -
898A GLN* 4.0 30.9 - - - +
916A THR* 3.5 42.6 - - - +
919A SER* 3.2 16.0 - - - +
920A VAL* 3.8 17.6 - - + +
971A PRO* 5.4 1.6 - - - +
993A ALA* 3.2 22.4 + - - +
994A ILE 4.1 3.4 - - - +
995A VAL 3.5 0.2 - - - -
996A GLU* 1.3 76.4 - - - +
998A ALA* 1.3 58.4 + - - +
999A GLY 3.2 1.3 + - - -
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Residues in contact with ALA 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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919A SER* 3.5 18.2 - - - +
971A PRO* 3.3 13.7 - - - +
972A LEU* 3.5 9.0 + - + +
973A PHE* 2.8 56.1 + - + +
994A ILE 3.4 9.3 + - - +
995A VAL 3.2 2.6 + - - +
996A GLU 3.0 1.4 - - - -
997A CYS* 1.3 79.1 - - - +
999A GLY* 1.3 55.6 - - - +
1000A GLY 3.4 2.0 - - - -
1056A VAL* 4.0 9.9 - - + -
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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