Contacts of the helix formed by residues 1238 - 1249 (chain K) in PDB entry 3F5P
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 PRO1238 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108K SER 5.7 0.4 - - - -
1109K LEU* 3.8 45.5 - - + +
1112K MET* 4.8 13.9 - - + -
1236K ASN 3.4 9.2 - - - +
1237K CYS* 1.3 92.2 - - + +
1239K ASP* 1.3 68.9 + - - +
1240K MET* 3.0 6.0 + - + +
1241K LEU* 3.1 15.7 + - + +
1242K PHE* 3.2 10.0 + - - +
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Residues in contact with ASP1239 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1233K LYS* 2.9 30.5 + - - +
1237K CYS 3.2 1.5 + - - -
1238K PRO* 1.3 72.7 - - - +
1240K MET* 1.3 61.6 + - - +
1242K PHE* 3.7 1.2 + - - +
1243K GLU* 3.1 32.8 + - - +
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Residues in contact with MET1240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109K LEU* 4.2 17.3 - - + -
1113K ILE* 3.3 28.3 - - + -
1238K PRO* 2.9 1.7 - - + +
1239K ASP* 1.3 78.6 - - - +
1241K LEU* 1.3 70.5 + - + +
1243K GLU* 3.2 3.8 + - - +
1244K LEU* 3.1 35.5 + - + +
1266K ILE* 3.7 29.8 - - + -
981M PHE* 3.6 51.1 - - + +
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Residues in contact with LEU1241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109K LEU* 4.8 4.3 - - + -
1112K MET* 3.4 50.7 - - + -
1113K ILE* 4.8 11.4 - - + +
1116K ALA* 5.1 5.2 - - + -
1202K LEU* 4.3 27.8 - - + +
1205K ILE* 5.3 1.1 - - + -
1206K ALA* 4.6 2.5 - - + -
1237K CYS* 4.0 6.7 - - - -
1238K PRO* 3.1 17.6 + - + +
1240K MET* 1.3 87.9 - - + +
1242K PHE* 1.3 61.9 + - - +
1244K LEU* 3.2 16.1 + - + +
1245K MET* 3.2 39.7 + - + +
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Residues in contact with PHE1242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203K TRP* 5.3 0.2 - + - -
1230K LEU* 6.1 2.7 - - + -
1231K LEU 4.0 13.7 - - - -
1232K ASP* 3.9 4.3 - - - -
1233K LYS* 3.3 67.8 - - + -
1234K PRO* 3.9 7.0 - - + -
1237K CYS* 3.9 9.1 - - - -
1238K PRO 3.2 7.7 + - - +
1239K ASP 4.2 2.2 - - - +
1241K LEU* 1.3 79.5 - - - +
1243K GLU* 1.3 68.1 + - - +
1245K MET* 3.4 16.6 + - + +
1246K ARG* 3.1 51.9 + - + +
1249K TRP* 4.1 13.7 - + - -
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Residues in contact with GLU1243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233K LYS* 5.5 1.6 + - - -
1239K ASP* 3.1 26.5 + - - +
1240K MET* 3.5 7.9 - - - +
1241K LEU 3.1 0.6 - - - -
1242K PHE* 1.3 80.8 - - - +
1244K LEU* 1.3 66.3 + - - +
1246K ARG* 2.5 47.2 + - - +
1247K MET* 3.0 36.8 + - + +
981M PHE* 4.0 22.2 - - + +
982M SER* 5.0 0.9 - - - -
1041M MET* 3.7 14.2 - - + +
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Residues in contact with LEU1244 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113K ILE* 6.5 0.2 - - + -
1116K ALA* 5.3 5.2 - - + -
1198K PHE* 4.9 0.9 - - + -
1202K LEU* 3.8 21.3 - - + -
1240K MET* 3.1 24.5 + - + +
1241K LEU* 3.2 17.3 - - + +
1243K GLU* 1.3 73.6 - - - +
1245K MET* 1.3 66.6 + - - +
1247K MET* 2.9 29.2 + - + +
1248K CYS* 3.0 23.9 + - - -
1257K PRO* 5.3 1.6 - - + -
1262K ILE* 3.9 35.4 - - + -
1265K SER* 5.0 2.0 - - - +
1266K ILE* 5.1 6.3 - - + -
981M PHE* 4.0 23.1 - - + -
986M VAL* 4.9 3.8 - - + -
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Residues in contact with MET1245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199K GLY* 3.7 13.0 - - - +
1202K LEU* 3.6 35.8 - - + +
1203K TRP* 3.6 27.4 - - - +
1206K ALA* 4.1 2.7 - - + -
1234K PRO* 5.0 0.2 - - - -
1237K CYS* 4.0 16.2 - - - -
1241K LEU* 3.2 32.1 + - + +
1242K PHE* 3.5 20.0 - - - +
1243K GLU 3.4 0.2 - - - -
1244K LEU* 1.3 76.0 - - - +
1246K ARG* 1.3 64.3 + - - +
1248K CYS* 2.9 12.3 + - - +
1249K TRP* 2.9 52.2 + - + -
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Residues in contact with ARG1246 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1230K LEU* 5.4 13.5 - - + +
1242K PHE* 3.1 47.2 + - + +
1243K GLU* 2.5 41.0 + - - +
1244K LEU 3.2 0.6 - - - -
1245K MET* 1.3 75.4 - - - +
1247K MET* 1.3 60.5 + - - +
1249K TRP* 3.3 20.2 + - + +
1250K GLN* 2.9 19.5 + - - +
1041M MET* 4.0 35.3 - - - +
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Residues in contact with MET1247 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1243K GLU* 3.0 29.2 - - + +
1244K LEU* 2.9 13.7 + - + +
1246K ARG* 1.3 76.1 - - - +
1248K CYS* 1.3 63.6 + - - +
1249K TRP 3.0 1.6 + - - -
1250K GLN* 3.1 27.6 + - - +
1256K ARG* 3.7 0.5 - - - +
1257K PRO* 3.6 17.7 - - + +
981M PHE* 3.5 30.3 - - + -
982M SER* 3.6 21.3 - - - +
983M ALA* 3.9 9.0 - - - +
986M VAL* 3.1 28.7 - - - -
987M TYR* 3.7 20.5 + - + +
1041M MET* 3.9 13.2 - - + -
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Residues in contact with CYS1248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195K VAL* 3.7 22.2 - - + +
1196K TRP* 3.6 11.4 - - - -
1198K PHE* 3.9 15.9 - - - -
1199K GLY* 3.9 14.4 - - - -
1202K LEU* 4.9 1.1 - - - -
1244K LEU* 3.0 21.0 + - - -
1245K MET 2.9 7.5 + - - +
1247K MET* 1.3 75.5 - - - +
1249K TRP* 1.3 58.3 + - + +
1250K GLN 3.3 0.7 - - - -
1256K ARG* 3.2 23.0 + - - -
1257K PRO* 4.0 11.0 - - - +
1262K ILE* 3.8 29.6 - - - -
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Residues in contact with TRP1249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196K TRP* 3.0 64.9 + + + -
1199K GLY 3.4 25.7 - - - -
1200K VAL* 3.7 8.3 - - - +
1203K TRP* 3.8 12.8 - + + -
1213K TYR* 5.8 0.2 - - - -
1230K LEU* 3.8 31.9 - - + +
1231K LEU* 3.6 54.7 - - + -
1242K PHE* 4.1 11.7 - + - -
1245K MET* 2.9 37.9 + - + +
1246K ARG* 3.3 12.1 + - + +
1247K MET 3.0 0.4 - - - -
1248K CYS* 1.3 80.4 - - + +
1250K GLN* 1.3 68.3 + - - +
1251K TYR* 2.9 4.3 + - - +
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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