Contacts of the helix formed by residues 93 - 111 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922 SER* 1.3 78.2 + - - +
942 PRO* 1.3 67.4 - - - -
952 ALA 3.3 1.8 - - - -
962 LEU* 2.8 29.4 + - - +
972 VAL* 3.2 14.9 + - - +
1332 VAL* 4.5 10.5 - - - -
644 THR* 4.5 0.9 - - - -
654 GLN* 5.3 2.2 - - - -
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Residues in contact with PRO 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932 GLY* 1.3 83.9 - - - -
952 ALA* 1.3 63.4 + - - +
972 VAL* 3.0 6.1 + - + +
982 ASN* 2.9 25.7 + - - +
1332 VAL* 3.8 25.0 - - + -
644 THR* 3.3 16.2 - - + +
654 GLN* 3.4 38.8 - - - +
674 GLY* 3.9 11.9 - - - +
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Residues in contact with ALA 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 ILE* 3.6 22.6 - - + +
932 GLY 3.1 0.6 + - - -
942 PRO* 1.3 79.6 - - - +
962 LEU* 1.3 58.1 + - - +
982 ASN* 3.3 2.2 + - - +
992 MET* 3.0 24.3 + - - +
644 THR* 3.2 17.9 + - + +
674 GLY* 3.5 15.7 - - - -
684 ILE 3.6 22.7 - - - +
694 THR* 3.4 14.0 - - + +
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Residues in contact with LEU 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832 VAL* 4.5 3.8 - - + +
862 ALA* 3.8 32.8 - - + +
872 LEU* 3.6 40.2 - - + +
902 ILE* 4.0 6.0 - - + +
912 GLY 3.4 12.3 + - - +
922 SER* 3.8 11.9 - - - -
932 GLY 2.8 15.8 + - - +
952 ALA* 1.3 71.3 - - - +
972 VAL* 1.3 63.6 + - + +
992 MET* 3.1 5.7 + - + +
1002 ILE* 2.8 50.2 + - + +
1262 THR* 4.8 10.3 - - + -
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Residues in contact with VAL 97 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932 GLY* 3.2 8.7 + - - +
942 PRO 3.0 8.0 + - - +
962 LEU* 1.3 78.7 - - + +
982 ASN* 1.3 65.8 + - - +
1002 ILE* 3.2 6.1 + - + +
1012 ASN* 2.9 28.1 + - - +
1302 THR* 3.5 20.4 + - - +
1312 GLY 3.7 26.9 - - - +
1322 TYR* 4.2 6.5 - - - +
1332 VAL* 3.8 34.1 - - + +
1342 SER 5.2 0.7 - - - +
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Residues in contact with ASN 98 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091 SER 3.5 22.9 - - - +
1101 ALA* 3.6 3.6 - - - +
1121 ASN* 5.1 9.6 - - - +
942 PRO* 2.9 13.3 + - - +
952 ALA* 3.4 8.5 - - - +
962 LEU 3.2 0.2 - - - -
972 VAL* 1.3 80.8 - - - +
992 MET* 1.3 63.9 + - - +
1012 ASN* 3.5 8.8 + - - +
1022 GLY 3.3 13.5 + - - -
674 GLY* 3.1 35.4 + - - -
694 THR* 4.4 7.9 - - + -
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Residues in contact with MET 99 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061 TYR* 4.6 13.5 - - - +
1101 ALA* 3.9 20.0 + - - +
1111 PHE* 3.7 31.2 - - + -
822 LYS* 5.9 2.5 - - - -
862 ALA* 3.8 24.5 - - + -
902 ILE* 3.8 22.9 - - + -
952 ALA 3.0 12.6 + - - +
962 LEU* 3.1 13.2 + - + +
982 ASN* 1.3 77.1 - - - +
1002 ILE* 1.3 59.1 + - + +
1022 GLY* 3.2 4.0 + - - -
1032 LEU* 2.9 34.1 + - + +
694 THR* 4.7 5.6 - - + -
237 A 4.1 12.8 - - - +
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Residues in contact with ILE 100 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792 PHE* 5.1 1.1 - - + -
832 VAL* 4.3 22.4 - - + -
962 LEU* 2.8 48.1 + - + +
972 VAL* 4.7 3.1 - - + -
992 MET* 1.3 74.1 - - + +
1012 ASN* 1.3 58.1 + - - +
1032 LEU* 4.1 6.3 - - + -
1042 LYS* 2.7 34.0 + - + +
1222 VAL* 4.3 20.2 - - + -
1262 THR* 4.1 24.5 - - + -
1302 THR* 3.6 34.5 - - + +
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Residues in contact with ASN 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091 SER* 4.2 7.5 + - - +
972 VAL* 2.9 23.2 + - - +
982 ASN* 3.7 11.2 + - - +
1002 ILE* 1.3 75.6 - - - +
1022 GLY* 1.3 60.8 + - - +
1042 LYS* 3.8 3.4 - - - +
1052 GLY* 3.2 19.1 + - - -
1302 THR* 2.5 31.2 + - - +
1312 GLY* 2.9 33.4 + - - -
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Residues in contact with GLY 102 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051 GLY 4.2 2.8 - - - -
1061 TYR* 3.7 11.6 + - - -
1091 SER* 2.9 25.2 + - - -
1101 ALA* 4.1 11.0 - - - -
982 ASN 3.3 4.4 + - - -
992 MET 3.2 6.2 + - - -
1012 ASN* 1.3 75.7 - - - +
1032 LEU* 1.3 58.8 + - - +
1052 GLY* 3.4 1.5 + - - -
1062 TYR* 2.9 29.8 + - - +
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Residues in contact with LEU 103 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061 TYR* 4.0 11.7 - - + -
792 PHE* 3.7 11.2 - - + -
822 LYS* 3.5 51.6 - - + +
832 VAL* 3.7 33.4 - - + +
992 MET* 2.9 25.1 + - + +
1002 ILE* 3.6 7.6 - - + +
1022 GLY* 1.3 74.5 - - - +
1042 LYS* 1.3 66.2 + - - +
1062 TYR* 3.2 9.3 - - + +
1072 TYR* 3.0 38.0 + - + -
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Residues in contact with LYS 104 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792 PHE* 3.8 17.7 - - + -
1002 ILE* 2.7 23.8 + - + +
1012 ASN* 3.8 4.5 - - - +
1032 LEU* 1.3 74.1 - - - +
1052 GLY* 1.3 63.3 + - - +
1072 TYR* 3.1 4.7 + - - +
1082 ILE* 3.0 47.5 + - + +
1152 PRO* 4.4 12.8 - - - +
1182 LEU* 4.0 12.7 - - + +
1192 ASP* 2.7 40.6 + - - +
1222 VAL* 6.0 1.3 - - + -
1302 THR* 4.3 19.4 - - + +
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Residues in contact with GLY 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021 GLY* 5.0 1.1 - - - -
1051 GLY* 5.9 3.1 - - - -
1061 TYR 5.7 0.2 - - - -
1012 ASN 3.2 12.7 + - - -
1022 GLY* 3.8 2.5 - - - -
1042 LYS* 1.3 78.3 - - - +
1062 TYR* 1.3 63.1 + - - +
1082 ILE* 3.2 12.8 + - - +
1092 SER* 3.1 28.0 + - - -
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Residues in contact with TYR 106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821 LYS* 2.7 33.8 + - - -
991 MET* 4.7 3.8 - - - -
1021 GLY 3.5 27.1 + - - -
1031 LEU* 3.9 14.6 - - + -
1061 TYR* 3.7 24.8 - + + +
822 LYS* 5.0 5.8 - - - -
1022 GLY 2.9 18.8 + - - +
1032 LEU* 3.2 14.6 - - + +
1052 GLY* 1.3 75.0 - - - +
1072 TYR* 1.3 79.6 + + - +
1092 SER* 3.7 0.2 + - - -
1102 ALA* 2.8 46.7 + - + +
1112 PHE* 3.7 28.1 - + - -
3178 A 3.3 16.7 + - - -
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Residues in contact with TYR 107 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752 ILE* 3.5 38.8 - - + -
782 GLY* 3.5 4.9 - - - -
792 PHE* 3.5 39.5 + + + -
822 LYS* 4.6 4.9 - - + -
1032 LEU* 3.0 29.0 + - + +
1042 LYS 3.8 6.1 - - - +
1062 TYR* 1.3 95.6 - + - +
1082 ILE* 1.3 66.1 + - - +
1112 PHE* 3.0 46.5 + + - -
1132 ALA* 3.1 22.0 + - + +
1182 LEU* 4.4 2.2 - - + -
3168 T 4.4 6.2 - - + +
3178 A 3.4 25.1 + - - -
71y PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042 LYS* 3.0 46.5 + - + +
1052 GLY* 3.2 10.5 + - - +
1072 TYR* 1.3 76.1 - - - +
1092 SER* 1.3 63.1 + - - +
1122 ASN* 3.0 25.3 - - - +
1132 ALA* 3.4 16.1 + - - +
1152 PRO* 3.9 25.8 - - + -
1182 LEU* 3.3 16.4 - - + -
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Residues in contact with SER 109 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981 ASN* 3.5 18.7 - - - +
1011 ASN* 4.2 7.1 + - - +
1021 GLY* 3.0 27.7 - - - -
1052 GLY 3.1 11.7 + - - -
1082 ILE* 1.3 82.2 - - - +
1102 ALA* 1.3 63.7 + - - +
1112 PHE 3.4 0.4 - - - -
1122 ASN* 4.0 10.9 - - - +
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Residues in contact with ALA 110 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981 ASN* 3.7 13.2 - - - +
991 MET* 4.2 14.9 - - - +
1021 GLY* 4.1 11.2 - - - -
1062 TYR* 2.8 36.2 + - + +
1092 SER* 1.3 75.7 + - - +
1112 PHE* 1.3 69.8 + - + +
1122 ASN* 5.2 1.1 - - - -
69y THR* 2.6 33.8 + - - +
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Residues in contact with PHE 111 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821 LYS* 6.1 0.2 - - - -
991 MET* 3.8 24.5 - - + -
752 ILE* 4.6 14.1 - - + +
1062 TYR* 3.7 37.2 - + - -
1072 TYR* 3.0 46.0 + + + +
1102 ALA* 1.3 80.3 - - + +
1122 ASN* 1.3 74.3 + - - +
1132 ALA* 3.2 2.2 + - - +
3168 T 3.6 39.0 - - - -
69y THR* 3.4 18.2 - - - +
70y GLY* 3.6 18.2 - - - -
71y PRO* 4.6 2.9 - - + -
72y ASN* 3.2 17.8 + - - +
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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
------------------------------------------------------------
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