Contacts of the helix formed by residues 1118 - 1130 (chain C) in PDB entry 5UH8
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 PRO1118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089C LEU 4.3 3.8 - - - +
1090C THR* 4.1 13.5 - - + -
1094C ASP* 3.2 25.8 - - - +
1095C ASP* 4.8 2.4 - - + -
1116C GLY 3.6 6.7 - - - +
1117C ILE* 1.3 95.8 - - + +
1119C GLU* 1.3 65.1 + - - +
1121C PHE* 3.1 22.4 + - + +
1122C LYS 3.4 4.0 + - - -
417D LEU* 5.7 0.2 - - + -
420D LYS* 4.5 8.1 - - - +
1253D ILE 4.2 6.1 - - - +
1254D ILE 3.3 32.1 - - - +
1255D GLY* 4.1 8.1 - - - -
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Residues in contact with GLU1119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053C THR 4.8 0.4 - - - +
1054C GLN* 4.2 10.5 - - + -
1094C ASP* 2.6 25.5 + - - +
1096C THR* 3.3 22.7 + - - +
1117C ILE 3.3 4.9 + - - +
1118C PRO* 1.3 71.3 - - - +
1120C SER* 1.3 59.7 + - - +
1122C LYS* 3.0 34.6 + - - +
1123C VAL* 3.1 13.7 + - - +
1148C ARG* 3.0 25.7 + - - -
86D LYS* 3.5 15.2 + - - -
89D ARG* 2.7 39.1 + - - +
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Residues in contact with SER1120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053C THR* 4.0 17.0 + - - +
1055C GLN* 4.1 4.1 + - - -
1094C ASP* 2.5 29.7 + - - -
1118C PRO* 4.7 0.2 - - - -
1119C GLU* 1.3 72.4 - - - +
1121C PHE* 1.3 61.7 + - - +
1123C VAL* 3.1 24.6 + - - +
1124C LEU* 3.2 6.9 + - - +
412D ARG* 4.4 7.7 - - - +
416D ASN* 3.8 17.7 + - - +
417D LEU* 3.4 22.4 - - - +
420D LYS* 4.2 5.8 - - - -
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Residues in contact with PHE1121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117C ILE* 5.0 11.4 - - + -
1118C PRO* 3.1 19.0 + - + +
1120C SER* 1.3 79.3 - - - +
1122C LYS* 1.3 64.7 + - + +
1124C LEU* 3.1 23.2 + - + +
1125C LEU* 3.2 50.0 + - + +
1137C VAL* 5.2 4.9 - - + -
1147C LEU* 5.4 4.0 - - + -
7D PHE* 5.6 7.6 - + - -
10D LEU* 4.2 16.6 - - + -
417D LEU* 4.0 7.0 - - + +
1221D LEU* 4.8 5.2 - - + -
1253D ILE* 3.5 41.3 - - + +
1254D ILE* 3.7 31.9 - - + -
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Residues in contact with LYS1122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117C ILE* 3.3 44.0 + - + +
1118C PRO 3.4 2.4 + - - +
1119C GLU* 3.0 29.8 + - - +
1121C PHE* 1.3 81.2 - - + +
1123C VAL* 1.3 62.2 + - + +
1125C LEU* 3.4 8.3 + - - +
1126C LYS* 3.2 27.3 + - + +
1147C LEU* 4.2 29.2 - - + +
1148C ARG* 3.5 44.4 - - + +
3D ASP* 5.0 8.2 + - - -
89D ARG* 5.8 0.7 - - - +
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Residues in contact with VAL1123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052C ILE* 3.9 25.8 - - + +
1053C THR* 4.8 2.7 - - - -
1119C GLU 3.1 16.3 + - - +
1120C SER* 3.1 15.0 + - - +
1122C LYS* 1.3 77.6 - - - +
1124C LEU* 1.3 50.5 + - - +
1126C LYS* 3.0 8.8 + - - +
1127C GLU* 2.8 45.5 + - + +
89D ARG* 4.2 7.6 - - - +
324D LEU* 4.1 26.7 - - + -
412D ARG* 3.7 26.5 - - - +
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Residues in contact with LEU1124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120C SER 3.2 5.3 + - - +
1121C PHE* 3.1 28.2 + - + +
1123C VAL* 1.3 79.7 - - - +
1125C LEU* 1.3 60.1 + - + +
1127C GLU* 3.0 7.5 + - - +
1128C LEU* 2.8 44.5 + - + +
406D LEU* 3.7 29.6 - - + -
412D ARG* 4.0 14.1 - - + +
413D PHE* 3.6 37.0 - - + -
417D LEU* 3.6 18.6 - - + -
1221D LEU* 5.0 5.4 - - + -
1253D ILE* 5.0 1.8 - - + -
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Residues in contact with LEU1125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121C PHE* 3.2 46.9 + - + +
1122C LYS* 3.9 7.9 - - - +
1123C VAL 3.3 0.4 - - - -
1124C LEU* 1.3 83.3 - - + +
1126C LYS* 1.3 61.9 + - + +
1128C LEU* 3.9 14.9 - - + +
1129C GLN* 3.2 34.2 + - - +
1135C VAL* 3.7 30.9 - - + +
1137C VAL* 3.8 13.7 - - + -
1147C LEU* 3.6 31.6 - - + -
10D LEU* 4.6 6.1 - - + -
1220D TRP* 5.7 0.9 - - + -
1221D LEU* 6.6 0.4 - - + -
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Residues in contact with LYS1126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122C LYS* 3.2 15.8 + - + +
1123C VAL* 3.0 9.3 + - - +
1125C LEU* 1.3 80.0 - - - +
1127C GLU* 1.3 61.6 + - - +
1128C LEU 3.3 0.4 - - - -
1129C GLN* 3.5 26.3 + - - +
1130C SER* 3.5 11.1 + - - -
1147C LEU* 6.5 0.4 - - - -
1149C GLU* 5.2 7.4 - - - +
89D ARG 4.0 14.8 - - - +
90D GLU* 3.2 36.5 + - - +
92D MET* 3.3 40.9 - - + +
320D ILE* 4.5 5.1 - - - +
321D PRO* 4.8 2.5 - - + -
324D LEU* 3.8 18.2 - - + -
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Residues in contact with GLU1127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052C ILE* 5.7 0.3 - - - +
1123C VAL* 2.8 24.1 + - + +
1124C LEU* 3.0 7.5 + - - +
1126C LYS* 1.3 78.9 - - + +
1128C LEU* 1.3 60.7 + - - +
1130C SER* 2.6 20.2 + - - -
1131C LEU* 3.9 15.1 + - - +
320D ILE* 4.3 17.1 - - + +
324D LEU* 5.5 1.1 - - + +
402D LEU* 5.2 4.1 - - + +
405D LEU* 3.2 30.1 - - + +
406D LEU* 3.6 25.3 - - + +
412D ARG* 2.9 47.7 + - - +
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Residues in contact with LEU1128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124C LEU* 2.8 37.5 + - + +
1125C LEU* 4.3 10.3 - - + +
1127C GLU* 1.3 76.7 - - - +
1129C GLN* 1.3 65.5 + - - +
1130C SER 3.2 0.2 - - - -
1131C LEU* 3.2 11.3 + - + +
1133C LEU* 3.2 46.1 + - + +
1135C VAL* 3.9 29.2 - - + -
12D ILE* 5.0 0.7 - - + -
406D LEU* 3.9 15.7 - - + -
413D PHE* 5.4 3.8 - - + -
1220D TRP* 4.2 23.3 - - + -
1233D LEU* 3.9 21.1 - - + -
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Residues in contact with GLN1129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125C LEU* 3.2 23.3 + - - +
1126C LYS* 3.5 24.5 + - - +
1128C LEU* 1.3 77.8 - - - +
1130C SER* 1.3 62.0 + - - +
1132C CYS* 3.1 10.9 + - - -
1133C LEU 3.9 10.3 + - - +
1135C VAL* 4.6 16.8 + - + +
23D TRP* 3.1 66.3 + - + +
92D MET* 3.6 25.5 - - + +
318D PRO* 3.6 3.2 - - - +
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Residues in contact with SER1130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126C LYS 3.5 10.2 + - - -
1127C GLU* 2.6 28.9 + - - -
1129C GLN* 1.3 78.8 - - - +
1131C LEU* 1.3 55.3 + - - +
1132C CYS 3.3 1.8 - - - -
92D MET* 4.3 2.0 - - - +
318D PRO* 3.4 22.7 - - - +
320D ILE* 4.1 22.8 - - - +
344D TYR* 4.4 4.5 - - - -
382D PHE* 3.3 18.9 - - - -
402D LEU* 3.5 27.9 - - - +
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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