Contacts of the helix formed by residues 93 - 111 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924 SER* 1.3 76.5 + - - +
944 PRO* 1.3 68.5 - - - -
954 ALA 3.3 1.8 - - - -
964 LEU* 2.8 28.7 + - - +
974 VAL* 3.2 16.3 + - - +
1334 VAL* 4.5 10.3 - - - -
646 THR* 4.5 0.7 - - - -
656 GLN* 5.3 2.5 - - - -
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Residues in contact with PRO 94 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934 GLY* 1.3 83.4 - - - -
954 ALA* 1.3 63.1 + - - +
974 VAL* 3.0 6.6 + - - +
984 ASN* 2.9 26.1 + - - +
1334 VAL* 3.8 26.6 - - + -
646 THR* 3.3 15.5 - - + +
656 GLN* 3.4 40.2 - - - +
666 TYR 4.7 0.2 - - - -
676 GLY* 3.9 11.0 - - - -
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Residues in contact with ALA 95 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904 ILE* 3.6 22.2 - - + -
934 GLY 3.1 0.6 + - - -
944 PRO* 1.3 78.3 - - - +
964 LEU* 1.3 58.1 + - - +
984 ASN* 3.3 1.8 + - - +
994 MET* 3.0 24.1 + - - +
646 THR* 3.2 18.8 + - - +
676 GLY* 3.6 15.7 - - - -
686 ILE 3.6 22.0 - - - +
696 THR* 3.4 14.3 - - + +
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Residues in contact with LEU 96 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834 VAL* 4.5 3.4 - - + +
864 ALA* 3.8 32.8 - - + +
874 LEU* 3.6 39.9 - - + +
904 ILE* 4.0 5.4 - - + +
914 GLY 3.4 12.3 - - - +
924 SER* 3.8 11.0 - - - -
934 GLY 2.8 16.5 + - - +
954 ALA* 1.3 72.1 - - - +
974 VAL* 1.3 62.8 + - + +
994 MET* 3.1 6.0 + - + +
1004 ILE* 2.8 50.2 + - + +
1264 THR* 4.8 10.5 - - + -
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Residues in contact with VAL 97 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934 GLY* 3.9 9.2 - - - +
944 PRO 3.0 8.6 + - - +
964 LEU* 1.3 79.1 - - + +
984 ASN* 1.3 65.9 + - - +
1004 ILE* 3.2 4.8 + - + -
1014 ASN* 2.9 27.8 + - - +
1304 THR* 3.5 21.1 + - - +
1314 GLY 3.7 26.7 - - - +
1324 TYR 4.2 6.5 - - - +
1334 VAL* 3.8 33.7 - - + +
1344 SER 5.2 0.9 - - - +
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Residues in contact with ASN 98 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093 SER 3.5 21.2 - - - +
1103 ALA* 3.6 4.4 - - - +
1123 ASN* 5.1 9.7 - - - +
944 PRO* 2.9 12.7 + - - +
954 ALA* 3.4 8.3 - - - +
974 VAL* 1.3 80.9 - - - +
994 MET* 1.3 64.2 + - - +
1014 ASN* 3.5 9.0 + - - +
1024 GLY 3.3 13.5 + - - -
676 GLY* 3.1 35.2 + - - -
696 THR* 4.4 7.6 - - + -
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Residues in contact with MET 99 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063 TYR* 4.6 12.6 - - - +
1103 ALA* 3.9 21.5 + - - +
1113 PHE* 3.7 31.9 - - + -
824 LYS* 5.9 2.7 - - - -
864 ALA* 3.8 23.3 - - + -
904 ILE* 3.8 22.7 - - + -
954 ALA 3.0 12.8 + - - +
964 LEU* 3.3 12.3 - - + +
984 ASN* 1.3 78.0 - - - +
1004 ILE* 1.3 59.9 + - + +
1024 GLY* 3.2 3.1 + - - -
1034 LEU* 2.9 34.2 + - + +
696 THR* 4.7 5.2 - - + -
117 A 4.1 13.2 - - - +
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Residues in contact with ILE 100 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794 PHE* 5.1 1.3 - - + -
834 VAL* 4.3 22.7 - - + -
864 ALA* 6.0 0.2 - - + -
964 LEU* 2.8 47.1 + - + +
974 VAL* 4.7 3.8 - - + -
994 MET* 1.3 75.3 - - + +
1014 ASN* 1.3 58.2 + - - +
1034 LEU* 4.1 7.0 - - + -
1044 LYS* 2.7 34.3 + - + +
1224 VAL* 4.3 20.0 - - + -
1264 THR* 4.1 24.2 - - + -
1304 THR* 3.6 34.3 - - + +
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Residues in contact with ASN 101 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093 SER* 4.2 7.6 + - - +
974 VAL* 2.9 23.1 + - - +
984 ASN* 3.7 10.3 + - - +
1004 ILE* 1.3 76.9 - - - +
1024 GLY* 1.3 60.9 + - - +
1044 LYS* 3.8 3.3 - - - +
1054 GLY* 3.2 18.9 + - - -
1304 THR* 2.5 31.2 + - - +
1314 GLY* 2.9 32.9 + - - -
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Residues in contact with GLY 102 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053 GLY 4.2 2.5 - - - +
1063 TYR* 3.7 12.5 + - - -
1093 SER* 2.9 24.8 + - - -
1103 ALA* 4.1 11.7 - - - -
984 ASN 3.3 4.6 + - - -
994 MET 3.2 5.8 + - - -
1014 ASN* 1.3 76.0 - - - +
1034 LEU* 1.3 59.7 + - - +
1054 GLY* 3.4 1.5 + - - -
1064 TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 103 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063 TYR* 4.0 11.3 - - + -
794 PHE* 3.7 10.8 - - + -
824 LYS* 3.5 51.8 - - + +
834 VAL* 3.7 33.9 - - + +
994 MET* 2.9 24.4 + - + +
1004 ILE* 3.6 8.3 - - + +
1024 GLY* 1.3 74.3 - - - +
1044 LYS* 1.3 65.9 + - - +
1064 TYR* 3.2 9.5 - - + +
1074 TYR* 3.0 37.7 + - + -
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Residues in contact with LYS 104 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794 PHE* 3.8 17.7 - - + -
1004 ILE* 2.7 22.8 + - + +
1014 ASN* 3.8 5.2 - - - +
1034 LEU* 1.3 73.3 - - - +
1054 GLY* 1.3 64.9 + - - +
1074 TYR* 3.1 5.2 + - - +
1084 ILE* 3.0 45.9 + - + +
1154 PRO* 4.4 13.4 - - - +
1184 LEU* 4.0 13.5 - - + +
1194 ASP* 2.7 39.3 + - - +
1224 VAL* 6.0 1.6 - - + -
1304 THR* 4.3 18.7 - - + +
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Residues in contact with GLY 105 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023 GLY* 5.0 0.9 - - - -
1053 GLY* 5.9 3.6 - - - -
1014 ASN 3.2 11.7 + - - -
1024 GLY 3.8 2.2 - - - -
1044 LYS* 1.3 77.2 - - - +
1064 TYR* 1.3 62.0 + - - +
1084 ILE* 3.2 11.9 + - - +
1094 SER* 3.0 29.8 + - - -
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Residues in contact with TYR 106 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823 LYS* 2.7 34.3 + - - -
993 MET* 4.7 3.3 - - - -
1023 GLY 3.5 26.6 + - - -
1033 LEU* 4.1 15.3 - - + -
1063 TYR* 3.7 25.9 - + + +
824 LYS* 5.0 6.3 - - - -
1024 GLY 2.9 19.1 + - - +
1034 LEU* 3.2 13.2 - - + +
1054 GLY* 1.3 75.1 - - - +
1074 TYR* 1.3 82.0 + + - +
1094 SER* 3.7 0.2 + - - -
1104 ALA* 2.8 44.8 + - + +
1114 PHE* 3.7 27.9 - + - -
3298 A 3.3 16.3 + - - -
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Residues in contact with TYR 107 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711 PRO* 6.5 1.1 - - + -
754 ILE* 3.5 38.1 - - + -
784 GLY* 3.5 4.7 - - - -
794 PHE* 3.5 38.9 + + + -
824 LYS* 4.6 4.5 - - + -
1034 LEU* 3.0 29.6 + - + +
1044 LYS 3.8 5.6 - - - +
1064 TYR* 1.3 96.1 - + - +
1084 ILE* 1.3 66.0 + - - +
1114 PHE* 3.0 46.7 + + - +
1134 ALA* 3.1 22.5 + - + +
1184 LEU* 4.4 2.9 - - + -
3288 T 4.4 6.2 + - + +
3298 A 3.4 24.6 + - - -
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Residues in contact with ILE 108 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044 LYS* 3.0 45.4 + - + +
1054 GLY* 3.2 11.0 + - - +
1074 TYR* 1.3 75.4 - - - +
1094 SER* 1.3 63.4 + - - +
1124 ASN* 3.0 26.0 - - - +
1134 ALA 3.5 16.3 - - - +
1154 PRO* 3.9 24.2 - - + -
1184 LEU* 3.3 17.3 - - + -
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Residues in contact with SER 109 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983 ASN* 3.5 18.2 - - - +
1013 ASN* 4.2 6.4 + - - -
1023 GLY* 3.0 29.1 - - - -
1054 GLY 3.0 11.1 + - - -
1084 ILE* 1.3 82.4 - - - +
1104 ALA* 1.3 64.5 + - - +
1114 PHE 3.4 0.2 - - - -
1124 ASN* 4.0 10.1 - - - +
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Residues in contact with ALA 110 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691 THR* 2.6 34.0 + - - +
983 ASN* 3.7 13.3 - - - +
993 MET* 4.2 14.6 - - - +
1023 GLY* 4.1 11.7 - - - -
1064 TYR* 2.8 36.0 + - + +
1094 SER* 1.3 77.2 + - - +
1114 PHE* 1.3 70.2 + - + +
1124 ASN* 5.2 0.9 + - - -
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Residues in contact with PHE 111 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691 THR* 3.4 17.3 - - - +
701 GLY* 3.6 19.1 - - - -
711 PRO* 4.6 2.9 - - + -
721 ASN* 3.2 19.4 + - - +
823 LYS* 6.1 0.4 - - - -
993 MET* 3.8 22.7 - - + -
754 ILE* 4.6 12.6 - - + +
1064 TYR* 3.7 37.7 - + - -
1074 TYR* 3.0 43.8 + + + +
1104 ALA* 1.3 81.6 - - + +
1124 ASN* 1.3 73.5 + - - +
1134 ALA* 3.2 2.4 + - - +
3288 T 3.6 39.5 - - - -
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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