Contacts of the helix formed by residues 97 - 103 (chain 7) in PDB entry 3J7Y
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 GLU 97 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937 MET* 5.9 0.7 - - - -
967 SER* 1.3 70.9 + - - +
987 TRP* 1.3 62.0 + - + +
997 TYR 3.2 2.0 - - - -
1007 CYS* 3.2 10.3 + - + +
1017 ARG* 2.9 62.3 + - - +
98T SER* 3.1 38.3 + - - -
100T ASP* 2.7 24.8 + - + +
101T GLN* 4.8 5.0 + - - +
138T SER* 3.2 27.4 + - - +
183T PRO* 5.2 3.6 - - - +
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Residues in contact with TRP 98 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070 ILE* 3.7 42.4 - - + -
1080 ASP* 4.5 3.1 - - - -
1090 VAL* 3.6 33.0 - - + -
1160 LEU* 5.1 13.0 - - + +
967 SER* 2.8 13.0 + - - +
977 GLU* 1.3 78.6 - - + +
997 TYR* 1.3 58.2 + - + +
1017 ARG* 3.2 16.2 + - + +
1027 LYS* 2.9 47.9 + - - +
100T ASP* 4.2 30.9 + - + +
101T GLN* 4.9 7.2 - - + +
104T ALA* 3.8 24.5 - - + +
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Residues in contact with TYR 99 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697 HIS* 4.5 5.2 + + - -
737 THR* 3.5 26.7 + - + +
747 ASP* 3.2 32.0 - - + +
927 ALA* 3.9 21.1 - - + +
957 LEU* 3.5 38.3 - - + +
967 SER* 3.2 24.1 + - - +
987 TRP* 1.3 78.4 - - + +
1007 CYS* 1.3 53.5 + - - +
1027 LYS* 5.1 1.6 - - - -
1037 SER* 2.7 45.4 + - - +
1277 PHE* 4.0 29.2 - + + -
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Residues in contact with CYS 100 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897 TYR* 3.8 33.9 + - + +
927 ALA* 3.5 7.9 - - - -
937 MET* 3.3 54.5 - - - -
967 SER 3.3 13.9 - - - -
977 GLU* 3.2 11.6 + - + +
997 TYR* 1.3 80.4 - - - +
1017 ARG* 1.3 64.2 + - + +
1027 LYS 3.5 0.2 + - - -
1037 SER* 3.8 15.2 + - - +
1157 MET* 6.0 0.3 - - - +
2707 PRO* 6.1 0.3 - - - +
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Residues in contact with ARG 101 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977 GLU* 2.9 49.5 + - - +
987 TRP* 3.5 17.9 - - + +
1007 CYS* 1.3 79.2 - - + +
1027 LYS* 1.3 66.1 + - + +
1037 SER 4.4 2.3 - - - +
1047 ILE* 5.7 1.0 - - - +
2747 ILE* 5.5 7.1 - - - +
3057 HIS* 4.2 19.0 + - - +
183T PRO* 6.2 2.0 - - - +
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Residues in contact with LYS 102 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080 ASP* 3.6 26.8 + - - +
1090 VAL* 3.7 38.5 + - + +
987 TRP* 2.9 27.0 + - - +
997 TYR* 4.4 1.6 - - - +
1017 ARG* 1.3 83.2 - - + +
1037 SER* 1.3 64.5 + - - +
1047 ILE* 3.6 7.8 - - - +
1297 THR* 3.4 38.4 - - + +
1307 PHE 4.8 0.2 + - - -
1317 LYS* 5.7 4.4 - - - +
3057 HIS* 4.5 25.6 - - + +
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Residues in contact with SER 103 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897 TYR* 5.8 0.2 - - - -
927 ALA* 4.3 0.3 - - - +
997 TYR* 2.7 31.7 + - - +
1007 CYS* 3.8 13.3 + - - +
1017 ARG 4.4 2.3 - - - +
1027 LYS* 1.3 73.8 - - - +
1047 ILE* 1.3 62.2 + - - +
1157 MET* 3.1 35.6 - - - +
1277 PHE* 3.8 28.2 - - - -
1287 LEU 3.6 7.0 - - - -
1297 THR* 4.6 1.7 - - - +
2707 PRO* 4.3 6.1 - - - +
2747 ILE* 5.3 1.6 - - - +
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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