Contacts of the helix formed by residues 1179 - 1192 (chain B) in PDB entry 5M64
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 PRO1179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A LYS* 4.1 5.8 - - - +
1641A ILE 5.6 1.8 - - - +
1642A VAL 3.8 18.6 - - - +
1643A VAL* 4.9 9.2 - - - +
1093B LEU* 4.1 16.4 - - + -
1097B ASP* 3.2 29.2 - - - +
1099B THR* 5.0 1.1 - - - +
1177B ALA 4.6 1.6 - - - +
1178B ILE* 1.3 100.5 - - + +
1180B PHE* 1.3 64.8 + - - +
1181B VAL* 5.2 0.4 - - + -
1182B LEU* 3.2 25.6 + - + +
1183B LYS* 3.2 16.8 + - - +
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Residues in contact with PHE1180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ARG* 6.0 1.8 - - - -
367A PHE* 4.2 5.7 - - + -
1056B THR* 3.7 18.1 - - - +
1057B MET* 3.4 45.3 - - + -
1096B SER 3.6 14.6 - - - -
1097B ASP* 2.3 41.8 + - - +
1098B TYR 3.4 22.2 - - - -
1099B THR* 3.4 31.4 - - + -
1179B PRO* 1.3 67.6 - - - +
1181B VAL* 1.3 56.8 + - - +
1183B LYS* 3.0 35.6 + - + +
1184B TYR* 3.0 11.6 + - - +
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Residues in contact with VAL1181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A HIS* 3.7 18.2 - - + -
471A MET* 3.5 30.3 - - + -
474A LYS* 4.5 5.6 - - - -
1056B THR* 3.4 17.3 - - - +
1058B GLN* 3.3 24.9 - - - +
1097B ASP* 3.2 22.2 - - - +
1179B PRO* 3.3 1.0 - - + -
1180B PHE* 1.3 72.8 - - - +
1182B LEU* 1.3 55.6 + - - +
1184B TYR* 3.2 16.8 + - + +
1185B LEU* 2.6 33.9 + - - +
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Residues in contact with LEU1182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1642A VAL* 3.3 28.0 - - + +
1643A VAL* 3.6 12.3 - - + -
1110B ILE* 4.4 10.3 - - + -
1178B ILE* 3.7 16.8 - - + -
1179B PRO* 3.2 32.3 + - + +
1180B PHE 3.2 0.4 - - - -
1181B VAL* 1.3 76.7 - - - +
1183B LYS* 1.3 59.6 + - - +
1184B TYR 3.1 0.2 - - - -
1185B LEU* 3.0 14.9 + - + -
1186B ASP* 2.8 35.7 + - + +
1198B TYR* 3.3 43.5 - - + +
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Residues in contact with LYS1183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 3.3 39.1 - - - +
366A ARG* 3.3 35.8 - - - +
367A PHE* 3.2 14.0 - - + -
1099B THR* 6.0 4.7 - - + -
1110B ILE* 5.1 19.5 - - + -
1111B LEU* 4.8 12.1 - - + +
1178B ILE* 5.1 4.7 - - + -
1179B PRO 3.2 10.8 + - - +
1180B PHE* 3.0 28.4 + - + +
1182B LEU* 1.3 77.3 - - - +
1184B TYR* 1.3 54.2 + - - +
1186B ASP* 2.8 19.9 - - - +
1187B SER* 3.6 6.2 - - - -
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Residues in contact with TYR1184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A PRO* 5.9 4.5 - - + -
367A PHE* 3.6 52.0 - + + -
382A GLN* 4.7 5.6 + - - -
459A ALA* 5.7 4.9 - - - +
460A LEU* 6.2 1.6 - - + -
471A MET* 6.2 2.5 - - + -
1055B LEU* 4.4 18.7 - - + +
1056B THR* 6.1 0.2 - - - -
1180B PHE 3.0 8.4 + - - +
1181B VAL* 3.6 19.5 - - + +
1183B LYS* 1.3 78.9 - - - +
1185B LEU* 1.3 62.2 + - - +
1186B ASP 3.5 0.2 - - - -
1187B SER* 3.6 5.1 - - - -
1188B GLU* 2.9 54.0 + - + +
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Residues in contact with LEU1185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A LEU* 4.8 9.9 - - + -
467A PHE* 4.4 28.5 - - + -
471A MET* 4.6 15.5 - - + -
1610A PHE* 5.0 12.1 - - + -
1642A VAL* 4.0 26.2 - - + -
1181B VAL 2.6 21.0 + - - +
1182B LEU* 3.0 14.7 + - + +
1184B TYR* 1.3 76.3 - - - +
1186B ASP* 1.3 58.2 + - - +
1188B GLU* 3.1 3.9 + - + +
1189B LEU* 2.9 48.3 + - + +
1198B TYR* 5.5 3.1 - - - +
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Residues in contact with ASP1186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B SER* 5.6 0.2 - - - -
1110B ILE* 4.0 15.8 + - - +
1111B LEU* 3.3 37.0 + - + +
1182B LEU* 2.8 21.4 + - + +
1183B LYS* 2.8 23.0 - - - +
1185B LEU* 1.3 74.1 - - - +
1187B SER* 1.3 65.6 + - - +
1189B LEU* 3.6 14.1 - - + +
1190B SER* 2.8 29.5 + - - -
1196B LEU* 4.6 24.0 - - + +
1198B TYR* 5.7 0.4 - - - +
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Residues in contact with SER1187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLN* 5.4 0.7 + - - -
363A PRO* 3.9 12.9 - - - +
364A PRO* 3.5 24.2 - - - +
367A PHE* 4.3 8.9 - - - -
1111B LEU* 3.7 16.2 - - - +
1183B LYS 3.6 14.4 - - - -
1184B TYR* 3.4 12.6 + - - -
1185B LEU 3.1 0.6 - - - -
1186B ASP* 1.3 82.8 + - - +
1188B GLU* 1.3 57.6 + - - +
1190B SER* 2.8 18.2 + - - -
1191B ALA* 3.1 15.9 + - - +
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Residues in contact with GLU1188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A PRO* 5.0 4.0 - - - +
382A GLN* 3.4 19.4 + - - -
456A VAL* 3.4 44.4 - - - +
459A ALA* 6.4 0.4 - - - -
460A LEU* 3.7 28.9 - - + -
1184B TYR* 2.9 45.4 + - + +
1185B LEU* 3.1 5.4 + - - +
1187B SER* 1.3 75.7 - - - +
1189B LEU* 1.3 63.8 + - - +
1191B ALA* 3.0 18.2 + - - +
1192B MET* 3.2 16.3 + - + +
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Residues in contact with LEU1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 6.1 3.1 - - + -
460A LEU* 5.6 2.7 - - + +
1622A LEU* 5.0 10.5 - - + -
1185B LEU* 2.9 42.3 + - + +
1186B ASP* 3.6 14.1 - - - +
1188B GLU* 1.3 76.9 - - - +
1190B SER* 1.3 61.9 + - - +
1192B MET* 3.1 24.5 - - - +
1194B ILE* 2.8 62.6 + - + +
1196B LEU* 3.6 37.2 - - + +
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Residues in contact with SER1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.6 8.2 - - - +
76A GLN* 4.6 7.8 + - - -
361A VAL* 3.2 18.4 - - - +
1111B LEU* 4.2 11.7 - - - +
1186B ASP 2.8 20.0 + - - -
1187B SER* 2.8 24.1 + - - -
1189B LEU* 1.3 76.3 - - - +
1191B ALA* 1.3 64.6 + - - +
1193B GLY* 3.2 13.2 + - - -
1194B ILE 3.2 13.4 + - - -
1195B ARG* 5.4 3.1 - - - -
1196B LEU 5.9 0.4 - - - -
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Residues in contact with ALA1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LEU* 5.5 6.4 - - - +
361A VAL* 3.7 32.1 + - + +
362A VAL 5.7 0.2 - - - -
363A PRO* 4.5 16.4 - - + -
382A GLN* 5.7 0.7 - - - +
437A PHE* 4.8 16.4 - - + -
438A ILE* 5.0 0.5 - - - +
456A VAL* 5.4 6.5 - - + -
1187B SER 3.1 14.6 + - - +
1188B GLU* 3.0 20.0 + - - +
1190B SER* 1.3 79.3 + - - +
1192B MET* 1.3 55.9 + - - +
1193B GLY 3.2 2.8 + - - -
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Residues in contact with MET1192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASN* 3.9 9.1 + - - -
89A LEU* 3.3 45.3 - - + +
357A MET* 5.5 0.9 - - - -
438A ILE* 3.9 26.1 - - + +
456A VAL* 5.3 7.6 - - + -
460A LEU* 6.4 1.1 - - + -
1619A CYS* 5.6 4.7 - - + +
1622A LEU* 3.8 28.0 - - + -
1188B GLU* 3.2 15.9 + - + +
1189B LEU* 3.1 29.2 - - - +
1191B ALA* 1.3 76.7 - - - +
1193B GLY* 1.3 57.0 + - - +
1194B ILE* 3.5 23.2 - - + +
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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