Contacts of the helix formed by residues 1114 - 1127 (chain O) in PDB entry 5Z3U
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 GLN1114 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ARG* 6.0 4.9 - - + +
53J G 5.1 2.5 + - - +
54J C 3.7 17.7 + - - -
1057O LYS* 6.2 1.9 - - - +
1064O VAL* 5.4 21.1 - - + -
1112O MET* 3.6 9.0 - - - +
1113O THR* 1.3 92.1 + - - +
1115O ILE* 1.3 60.1 + - + +
1117O ASP* 2.8 43.0 + - - +
1118O ILE* 3.8 7.2 + - + +
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Residues in contact with ILE1115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057O LYS* 5.9 2.2 - - - +
1060O ASN* 3.8 38.6 - - + +
1061O HIS* 5.4 9.6 - - + -
1064O VAL* 6.0 5.6 - - + -
1089O PHE* 5.4 8.3 - - + -
1110O PHE* 3.5 27.1 - - + -
1112O MET* 3.2 44.2 - - + +
1113O THR 2.7 5.5 + - - -
1114O GLN* 1.3 78.5 - - + +
1116O MET* 1.3 61.9 + - - +
1117O ASP 3.0 0.9 + - - -
1118O ILE* 3.2 12.6 + - + +
1119O MET* 2.9 22.1 + - + +
1181O PHE* 5.3 1.6 - - + -
1182O ASP* 4.6 3.4 - - - +
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Residues in contact with MET1116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110O PHE* 4.4 13.4 - - + -
1113O THR* 2.8 30.5 + - - +
1115O ILE* 1.3 76.7 - - - +
1117O ASP* 1.3 69.7 + - - +
1119O MET* 3.4 9.1 + - - +
1120O GLU* 2.8 57.8 + - + +
1132O ARG* 3.6 15.3 - - + +
1133O LEU 4.1 6.7 - - - +
1134O ASP* 3.2 48.5 - - + +
1160O ILE* 4.4 23.2 - - + +
1161O LEU 6.0 0.7 - - - +
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Residues in contact with ASP1117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS 5.0 1.1 - - - +
17B ARG 3.8 17.3 - - - +
18B HIS* 5.6 1.6 - - - -
19B ARG* 3.1 46.5 + - - +
1113O THR 5.1 0.3 - - - -
1114O GLN* 2.8 27.9 + - - +
1116O MET* 1.3 88.4 - - - +
1118O ILE* 1.3 63.5 + - + +
1120O GLU* 2.9 31.3 + - - +
1121O ASP* 3.0 15.1 + - - +
1132O ARG* 4.8 4.5 + - - -
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Residues in contact with ILE1118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG 5.8 0.2 - - - +
18B HIS* 4.5 17.3 - - + +
1061O HIS* 3.3 43.5 - - + +
1062O PRO 3.5 4.3 - - - +
1063O PHE* 3.4 34.1 - - + +
1064O VAL* 4.4 7.0 - - + +
1082O ILE* 5.3 8.5 - - + -
1089O PHE* 4.6 8.7 - - + -
1114O GLN* 4.7 9.0 - - + +
1115O ILE* 3.2 10.4 + - + +
1117O ASP* 1.3 78.1 - - + +
1119O MET* 1.3 57.0 + - - +
1121O ASP* 3.3 10.2 + - + +
1122O PHE* 2.9 27.3 + - + +
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Residues in contact with MET1119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089O PHE* 3.6 27.5 - - + -
1092O LEU* 4.1 11.4 - - + -
1108O ILE* 5.2 3.4 - - + -
1110O PHE* 3.9 14.8 - - + -
1115O ILE* 2.9 15.0 + - + +
1116O MET* 3.5 14.1 - - - +
1118O ILE* 1.3 77.7 - - - +
1120O GLU* 1.3 56.8 + - - +
1122O PHE* 3.1 25.7 + - - +
1123O LEU* 2.9 37.4 + - + +
1160O ILE* 4.0 15.0 - - + -
1181O PHE* 3.6 31.4 - - + -
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Residues in contact with GLU1120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS* 5.0 14.2 - - - +
17B ARG* 5.6 5.1 + - - +
1116O MET* 2.8 37.4 + - - +
1117O ASP* 2.9 13.3 + - - +
1119O MET* 1.3 76.2 - - - +
1121O ASP* 1.3 60.3 - - - +
1123O LEU* 3.1 4.8 + - - +
1124O ARG* 2.8 30.1 + - + +
1130O TYR* 3.1 35.5 + - + +
1132O ARG* 2.4 52.6 + - - +
1160O ILE* 4.5 6.7 - - + -
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Residues in contact with ASP1121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 2.9 48.3 - - - +
18B HIS* 3.1 37.4 + - + -
1078O THR* 4.3 10.9 - - + +
1117O ASP 3.0 12.8 + - - +
1118O ILE* 3.7 10.6 - - + +
1120O GLU* 1.3 77.9 - - - +
1122O PHE* 1.3 62.2 + - - +
1124O ARG* 2.9 11.2 + - + +
1125O TYR* 2.9 20.8 + - - +
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Residues in contact with PHE1122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082O ILE* 4.0 24.2 - - + -
1083O TRP* 3.8 28.7 - + + -
1089O PHE* 4.0 30.5 - + + -
1092O LEU* 3.5 26.2 - - + -
1093O ASP* 4.7 8.1 - - + -
1118O ILE* 2.9 16.1 + - + +
1119O MET* 3.1 29.3 + - - +
1121O ASP* 1.3 76.7 - - - +
1123O LEU* 1.3 56.5 - - + +
1125O TYR* 3.1 17.9 + + + +
1126O ILE* 2.9 53.9 + - + +
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Residues in contact with LEU1123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096O LEU* 6.1 0.4 - - + -
1108O ILE* 6.4 1.8 - - + -
1119O MET* 2.9 32.3 + - + +
1120O GLU 3.6 1.8 - - - +
1122O PHE* 1.3 72.5 - - + +
1124O ARG* 1.3 57.4 + - - +
1126O ILE* 2.7 30.9 + - + +
1127O ASN* 2.5 36.6 + - - -
1128O ILE* 4.2 12.0 - - + +
1130O TYR* 3.4 54.3 - - + -
1158O CYS* 5.6 11.0 - - + -
1160O ILE* 5.0 6.5 - - + -
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Residues in contact with ARG1124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 2.9 48.7 - - - +
1078O THR* 4.9 7.5 - - + +
1120O GLU* 2.8 27.2 + - + +
1121O ASP* 2.9 17.5 + - + +
1123O LEU* 1.3 74.6 - - - +
1125O TYR* 1.3 51.9 + - - +
1127O ASN* 2.7 25.7 - - - +
1130O TYR* 4.1 16.2 - - - +
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Residues in contact with TYR1125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078O THR* 4.2 34.4 - - + +
1079O ASN 5.5 2.2 - - - +
1083O TRP* 5.5 13.8 + + - -
1121O ASP 2.9 11.0 + - - +
1122O PHE* 3.4 20.2 - + + +
1123O LEU 3.1 0.2 - - - -
1124O ARG* 1.3 76.7 - - - +
1126O ILE* 1.3 73.5 + - + +
1127O ASN* 3.5 12.2 + - - -
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Residues in contact with ILE1126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092O LEU* 5.7 1.6 - - + -
1093O ASP* 6.3 0.4 - - - -
1096O LEU* 3.9 40.1 - - + +
1122O PHE* 2.9 47.3 + - + +
1123O LEU* 2.7 37.9 + - + +
1125O TYR* 1.3 83.3 - - + +
1127O ASN* 1.3 61.2 + - - +
1128O ILE* 3.2 39.5 + - + +
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Residues in contact with ASN1127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123O LEU 2.5 17.1 + - - -
1124O ARG* 2.7 27.0 - - - +
1125O TYR 3.6 9.9 + - - -
1126O ILE* 1.3 72.2 + - - +
1128O ILE* 1.3 62.0 + - + +
1129O LYS* 3.7 4.7 + - - +
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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