Contacts of the helix formed by residues 1238 - 1249 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1109I LEU* 3.9 42.4 - - + +
1112I MET* 4.9 14.8 - - + -
1206I ALA* 5.8 0.2 - - + -
1236I ASN 3.4 8.3 - - - +
1237I CYS* 1.3 92.5 - - - +
1239I ASP* 1.3 67.3 + - - +
1240I MET* 4.3 2.0 - - + +
1241I LEU* 3.1 20.6 + - + +
1242I PHE* 3.2 9.9 + - - +
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Residues in contact with ASP1239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233I LYS* 2.6 36.1 + - - +
1237I CYS 4.1 2.3 - - - +
1238I PRO* 1.3 71.1 - - - +
1240I MET* 1.3 61.6 + - - +
1242I PHE* 3.2 1.6 + - - +
1243I GLU* 3.0 34.5 + - - +
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Residues in contact with MET1240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109I LEU* 4.0 24.9 - - + -
1113I ILE* 3.6 34.3 - - + -
1238I PRO* 3.1 2.6 - - + +
1239I ASP* 1.3 79.7 - - - +
1241I LEU* 1.3 66.2 + - + +
1243I GLU* 3.5 3.9 + - - +
1244I LEU* 3.2 34.1 + - + +
1266I ILE* 3.8 20.4 - - + -
981J PHE* 3.5 48.0 - - + -
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Residues in contact with LEU1241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109I LEU* 4.7 5.8 - - + -
1112I MET* 3.4 50.9 - - + -
1113I ILE* 4.4 22.2 - - + -
1116I ALA* 5.0 3.1 - - + -
1202I LEU* 4.3 25.8 - - + +
1205I ILE* 5.2 0.9 - - + -
1206I ALA* 4.5 7.2 - - + -
1237I CYS* 4.0 7.0 - - - -
1238I PRO* 3.1 17.6 + - + +
1240I MET* 1.3 80.4 - - + +
1242I PHE* 1.3 63.2 + - - +
1244I LEU* 3.2 16.6 + - + +
1245I MET* 3.1 33.1 + - + +
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Residues in contact with PHE1242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230I LEU* 6.3 2.0 - - + -
1231I LEU 4.0 11.9 - - - -
1232I ASP* 4.0 5.4 - - - -
1233I LYS* 3.3 67.8 - - + -
1234I PRO* 4.0 2.5 - - + -
1237I CYS* 4.0 3.7 - - - -
1238I PRO 3.2 6.9 + - - +
1239I ASP 3.2 7.4 + - - +
1241I LEU* 1.3 77.3 - - - +
1243I GLU* 1.3 67.5 + - - +
1245I MET* 3.0 22.2 + - - +
1246I ARG* 2.9 53.4 + - + +
1249I TRP* 4.3 13.5 - + - -
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Residues in contact with GLU1243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233I LYS* 5.1 2.3 + - - -
1239I ASP* 3.0 31.4 + - - +
1240I MET* 3.8 5.6 - - - +
1242I PHE* 1.3 82.2 - - - +
1244I LEU* 1.3 59.8 + - - +
1246I ARG* 2.8 47.5 + - - +
1247I MET* 2.8 40.7 + - + +
981J PHE* 4.1 22.9 - - + +
982J SER* 5.1 2.2 - - - -
1041J MET* 3.6 14.3 - - + +
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Residues in contact with LEU1244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116I ALA* 5.3 5.8 - - + -
1198I PHE* 5.1 0.7 - - + -
1202I LEU* 3.8 21.8 - - + -
1240I MET* 3.2 27.3 + - + +
1241I LEU* 3.2 18.3 + - + +
1242I PHE 3.1 0.8 - - - -
1243I GLU* 1.3 74.5 - - - +
1245I MET* 1.3 65.2 + - - +
1247I MET* 3.2 20.3 + - + +
1248I CYS* 3.1 28.1 + - - -
1257I PRO* 5.4 1.1 - - + -
1262I ILE* 3.7 40.6 - - + -
1265I SER* 5.0 0.4 - - - +
1266I ILE* 4.9 6.5 - - + -
981J PHE* 4.1 18.6 - - + -
986J VAL* 4.9 3.6 - - + -
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Residues in contact with MET1245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199I GLY* 4.1 9.6 - - - +
1202I LEU* 3.9 15.9 - - + +
1203I TRP* 3.8 35.2 - - - +
1206I ALA* 4.0 6.3 - - + -
1234I PRO* 4.4 4.0 - - + -
1237I CYS* 3.9 26.0 - - - -
1241I LEU* 3.1 24.0 - - + +
1242I PHE* 3.0 15.2 + - - +
1244I LEU* 1.3 77.0 - - - +
1246I ARG* 1.3 63.8 + - - +
1248I CYS* 2.9 18.9 + - - +
1249I TRP* 2.9 56.2 + - + -
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Residues in contact with ARG1246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230I LEU* 5.6 12.3 - - + +
1242I PHE* 2.9 44.1 + - + +
1243I GLU* 2.8 33.7 + - - +
1244I LEU 3.3 0.4 - - - -
1245I MET* 1.3 75.9 - - - +
1247I MET* 1.3 61.7 + - - +
1249I TRP* 3.1 21.4 + - + +
1250I GLN* 3.2 17.2 + - - +
1040J SER* 6.0 0.6 - - - +
1041J MET* 3.5 42.2 - - - +
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Residues in contact with MET1247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243I GLU* 2.8 24.0 - - + +
1244I LEU* 3.5 11.4 - - - +
1245I MET 3.1 0.4 - - - -
1246I ARG* 1.3 72.2 - - - +
1248I CYS* 1.3 64.6 + - - +
1249I TRP 2.9 5.4 + - - -
1250I GLN* 3.2 26.4 + - - +
1256I ARG* 3.6 1.6 - - - +
1257I PRO* 3.5 17.6 - - + +
981J PHE* 3.7 27.4 - - + -
982J SER 3.8 1.8 - - - -
983J ALA* 3.6 26.0 - - - +
986J VAL* 3.3 26.9 - - + -
987J TYR* 3.8 28.1 + - + +
1041J MET* 4.0 16.6 - - + -
1045J ILE* 4.9 0.2 - - - -
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Residues in contact with CYS1248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195I VAL* 3.5 28.9 - - + +
1196I TRP* 3.8 11.1 - - - -
1198I PHE* 3.9 16.2 - - - -
1199I GLY* 3.9 14.6 - - - -
1202I LEU* 4.9 0.7 - - - -
1244I LEU* 3.1 22.5 + - - -
1245I MET 2.9 7.4 + - - +
1247I MET* 1.3 77.3 - - - +
1249I TRP* 1.3 57.8 + - + +
1250I GLN 3.5 0.2 - - - -
1256I ARG* 3.0 23.8 + - - -
1257I PRO* 4.1 2.9 - - - -
1262I ILE* 3.7 30.3 - - - -
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Residues in contact with TRP1249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196I TRP* 3.4 59.3 + + + -
1199I GLY* 3.4 26.9 - - - -
1200I VAL* 3.8 9.4 - - + +
1203I TRP* 4.0 4.9 - + + -
1213I TYR* 5.7 0.9 - - - -
1230I LEU* 4.0 32.5 - - + +
1231I LEU* 3.8 53.2 - - + -
1242I PHE* 4.3 11.4 - + - -
1245I MET* 2.9 46.5 + - + +
1246I ARG* 3.1 12.8 + - + +
1247I MET 2.9 1.4 - - - -
1248I CYS* 1.3 84.3 - - + +
1250I GLN* 1.3 67.6 + - - +
1251I TYR* 2.8 5.7 + - - +
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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