Contacts of the helix formed by residues 93 - 111 (chain 5) in PDB entry 3J9X
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 GLY 93 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643 THR* 4.6 0.9 - - - -
925 SER* 1.3 75.7 - - - +
945 PRO* 1.3 68.0 - - - -
955 ALA 3.3 1.8 - - - -
965 LEU* 2.7 29.9 + - - +
975 VAL* 3.1 15.3 + - - +
1335 VAL* 4.3 19.4 - - - +
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Residues in contact with PRO 94 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643 THR* 3.3 17.5 - - + +
653 GLN* 3.4 27.1 - - + +
663 TYR 4.6 0.7 - - - -
673 GLY* 3.8 10.8 - - - +
925 SER 4.6 0.2 - - - +
935 GLY* 1.3 83.3 - - - -
955 ALA* 1.3 63.8 + - - +
975 VAL* 3.0 12.2 + - + +
985 ASN* 2.9 25.9 + - - +
1335 VAL* 4.3 8.2 - - + -
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Residues in contact with ALA 95 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643 THR* 3.3 18.6 + - + +
673 GLY* 3.5 15.9 - - - -
683 ILE 3.7 20.4 - - - +
693 THR* 3.4 13.4 - - + +
905 ILE* 3.5 25.4 - - + -
935 GLY 3.1 0.6 + - - -
945 PRO* 1.3 78.6 - - - +
965 LEU* 1.3 61.2 + - - +
985 ASN* 3.3 1.5 + - - +
995 MET* 3.0 19.9 + - - +
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Residues in contact with LEU 96 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835 VAL* 4.3 5.4 - - + +
865 ALA* 3.9 28.9 - - + +
875 LEU* 3.8 37.7 - - + +
905 ILE* 4.2 4.9 - - + +
915 GLY 3.6 13.0 + - - +
925 SER* 3.9 11.2 - - - -
935 GLY 2.7 16.3 + - - +
955 ALA* 1.3 70.7 - - - +
975 VAL* 1.3 63.4 + - + +
995 MET* 3.1 5.7 + - + +
1005 ILE* 2.8 52.3 + - + +
1265 THR* 4.6 13.0 - - + -
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Residues in contact with VAL 97 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935 GLY* 3.8 7.4 - - - +
945 PRO* 3.0 9.8 + - + +
965 LEU* 1.3 79.3 - - + +
985 ASN* 1.3 66.5 + - - +
1005 ILE* 3.3 0.8 + - + -
1015 ASN* 3.1 33.9 + - - +
1305 THR* 3.4 25.2 + - - +
1315 GLY* 3.6 29.8 - - - +
1325 TYR 4.8 2.9 - - - +
1335 VAL* 3.7 30.7 - - + -
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Residues in contact with ASN 98 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673 GLY* 3.1 34.8 + - - -
693 THR* 4.4 7.6 - - + -
945 PRO* 2.9 12.4 + - - +
955 ALA* 3.5 8.1 - - - +
965 LEU 3.2 0.2 - - - -
975 VAL* 1.3 82.1 - - - +
995 MET* 1.3 63.0 + - - +
1015 ASN* 3.5 9.0 + - - +
1025 GLY 3.3 15.2 + - - -
1096 SER 3.5 22.3 - - - +
1106 ALA* 3.7 4.1 - - - +
1126 ASN* 5.2 9.1 + - - +
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Residues in contact with MET 99 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693 THR* 4.6 5.6 - - + -
825 LYS* 4.7 12.6 - - - +
835 VAL* 6.3 0.7 - - - -
865 ALA* 3.8 24.2 - - + -
905 ILE* 3.7 23.3 - - + -
955 ALA 3.0 13.6 + - - +
965 LEU* 3.3 13.2 - - + +
985 ASN* 1.3 78.1 - - - +
1005 ILE* 1.3 60.1 + - + +
1025 GLY* 3.2 3.6 + - - -
1035 LEU* 2.8 32.8 + - + +
1066 TYR* 4.7 9.6 - - - -
1106 ALA* 4.2 19.2 + - - +
1116 PHE* 3.8 29.6 - - + -
3408 T 4.1 11.4 - - - +
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Residues in contact with ILE 100 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795 PHE* 5.0 3.1 - - + -
835 VAL* 4.3 18.8 - - + -
965 LEU* 2.8 47.0 + - + +
975 VAL* 3.9 3.8 - - + +
995 MET* 1.3 74.6 - - + +
1015 ASN* 1.3 57.3 + - - +
1035 LEU* 3.5 6.9 - - + +
1045 LYS* 2.8 43.4 + - + +
1225 VAL* 4.2 15.9 - - + -
1265 THR* 4.1 22.0 - - + -
1305 THR* 3.5 34.3 - - + +
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Residues in contact with ASN 101 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975 VAL* 3.1 34.0 + - - +
985 ASN* 3.7 9.9 + - - +
1005 ILE* 1.3 78.2 - - - +
1025 GLY* 1.3 61.1 + - - +
1045 LYS* 3.5 8.4 + - - +
1055 GLY* 3.2 17.5 + - - -
1305 THR* 3.3 20.7 - - - +
1315 GLY* 4.3 7.5 + - - -
1096 SER* 4.2 8.4 + - - +
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Residues in contact with GLY 102 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985 ASN 3.3 4.4 + - - -
995 MET 3.2 5.6 + - - -
1015 ASN* 1.3 75.9 - - - +
1035 LEU* 1.3 61.0 + - - +
1055 GLY* 3.1 3.7 + - - -
1065 TYR 2.9 23.7 + - - -
1056 GLY 5.3 0.2 - - - -
1066 TYR* 3.5 20.7 - - - -
1096 SER* 3.0 24.3 + - - -
1106 ALA* 4.0 9.9 - - - -
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Residues in contact with LEU 103 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795 PHE* 3.6 17.3 - - + -
825 LYS* 3.5 47.1 - - + +
835 VAL* 3.6 31.2 - - + +
995 MET* 2.8 22.6 + - + +
1005 ILE* 3.5 9.2 - - + +
1025 GLY* 1.3 72.8 - - - +
1045 LYS* 1.3 64.5 + - - +
1065 TYR* 3.1 12.0 + - + +
1075 TYR* 3.0 40.8 + - + -
1066 TYR* 3.9 9.9 - - + -
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Residues in contact with LYS 104 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795 PHE* 3.8 28.0 - - + -
1005 ILE* 2.8 34.2 + - + +
1015 ASN* 3.7 7.7 + - - +
1035 LEU* 1.3 72.4 - - - +
1055 GLY* 1.3 58.6 + - - +
1075 TYR* 3.2 1.4 + - - +
1085 ILE* 2.8 53.9 + - + +
1155 PRO* 5.0 5.3 - - - +
1185 LEU* 4.8 5.8 - - + -
1195 ASP* 2.7 37.3 + - - +
1225 VAL* 5.0 2.0 - - + -
1295 PRO* 6.1 0.2 - - - +
1305 THR* 4.6 13.1 - - + +
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Residues in contact with GLY 105 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015 ASN 3.2 8.0 + - - -
1025 GLY* 3.1 8.0 + - - -
1045 LYS* 1.3 78.1 - - - +
1065 TYR* 1.3 57.6 + - - +
1085 ILE* 4.5 6.5 - - - +
1095 SER* 2.6 37.1 + - - -
1026 GLY 4.4 3.4 - - - -
1056 GLY* 5.9 2.5 - - - -
1066 TYR 5.3 1.8 - - - -
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Residues in contact with TYR 106 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825 LYS* 5.5 4.3 - - - -
1025 GLY 2.9 12.5 + - - +
1035 LEU* 3.2 15.7 - - + +
1055 GLY* 1.3 74.8 - - - +
1075 TYR* 1.3 86.2 + + - +
1105 ALA* 2.8 41.6 + - + +
1115 PHE* 3.7 30.4 - + - -
826 LYS* 2.8 40.2 + - - -
996 MET* 4.6 8.4 - - - +
1026 GLY 3.7 15.3 + - - -
1036 LEU* 4.0 13.0 - - + -
1066 TYR* 3.7 31.9 - + + -
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Residues in contact with TYR 107 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755 ILE* 3.5 38.6 - - + -
785 GLY* 3.5 20.5 + - - -
795 PHE* 3.7 30.1 - + + -
825 LYS* 5.2 2.4 - - + +
1035 LEU* 3.0 25.9 + - + +
1045 LYS 4.0 1.6 - - - +
1065 TYR* 1.3 99.9 - + - +
1085 ILE* 1.3 65.6 + - - +
1115 PHE* 3.1 41.0 + + + -
1135 ALA* 3.0 25.7 + - + +
1185 LEU* 4.4 8.1 - - + -
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Residues in contact with ILE 108 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045 LYS* 2.8 44.3 + - + +
1055 GLY* 4.1 5.8 - - - +
1075 TYR* 1.3 71.4 - - - +
1095 SER* 1.3 62.1 + - - +
1125 ASN* 3.1 25.5 - - - +
1135 ALA 3.6 17.0 - - - +
1155 PRO* 3.9 31.2 - - + -
1185 LEU* 3.3 21.5 - - + -
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Residues in contact with SER 109 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055 GLY 2.6 22.2 + - - -
1085 ILE* 1.3 82.7 - - - +
1105 ALA* 1.3 62.1 + - - +
1125 ASN* 4.0 10.2 - - - +
986 ASN* 3.5 16.9 - - - +
1016 ASN* 4.2 5.9 + - - +
1026 GLY* 2.9 21.6 - - - -
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Residues in contact with ALA 110 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065 TYR* 2.8 26.0 + - + +
1095 SER* 1.3 79.9 + - - +
1115 PHE* 1.3 74.8 + - + +
1125 ASN* 3.6 2.4 + - - -
986 ASN* 3.6 19.7 - - - +
996 MET* 3.9 38.4 + - - +
1026 GLY* 4.1 4.9 - - - -
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Residues in contact with PHE 111 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755 ILE* 4.8 21.7 - - + +
1065 TYR* 3.7 35.9 - + - -
1075 TYR* 3.1 48.4 + + + +
1105 ALA* 1.3 83.4 - - + +
1125 ASN* 1.3 75.2 + - - +
1135 ALA* 3.3 2.0 + - - +
996 MET* 3.7 31.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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