Contacts of the helix formed by residues 1238 - 1249 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106G PRO* 4.7 10.1 - - + -
1107G PRO 5.9 0.2 - - - +
1109G LEU* 3.9 40.6 - - + +
1112G MET* 5.1 7.9 - - - -
1236G ASN 3.4 9.0 - - - +
1237G CYS* 1.3 92.1 - - - +
1239G ASP* 1.3 69.0 + - - +
1240G MET* 3.0 5.0 + - + +
1241G LEU* 3.0 13.2 + - + +
1242G PHE 3.5 6.8 + - - -
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Residues in contact with ASP1239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233G LYS* 2.9 34.1 + - - +
1237G CYS 4.3 1.9 - - - +
1238G PRO* 1.3 70.9 - - - +
1240G MET* 1.3 56.8 + - - +
1242G PHE* 3.2 1.6 + - - -
1243G GLU* 2.8 43.6 + - - +
980H SER* 6.5 1.1 - - - -
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Residues in contact with MET1240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109G LEU* 4.1 25.4 - - + -
1113G ILE* 3.4 35.7 - - + -
1238G PRO* 3.0 2.8 + - + +
1239G ASP* 1.3 79.8 - - - +
1241G LEU* 1.3 66.1 + - - +
1243G GLU* 3.3 3.6 + - - +
1244G LEU* 3.1 29.3 + - + +
1266G ILE* 3.7 19.7 - - + -
981H PHE* 3.5 53.7 - - + +
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Residues in contact with LEU1241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109G LEU* 4.5 9.4 - - + -
1112G MET* 3.7 46.0 - - + -
1113G ILE* 4.3 22.7 - - + -
1116G ALA* 5.0 1.1 - - + -
1202G LEU* 4.0 33.4 - - + +
1205G ILE* 5.5 0.9 - - + -
1206G ALA* 4.3 2.7 - - + -
1237G CYS* 4.1 5.8 - - - -
1238G PRO* 3.0 12.3 + - + +
1240G MET* 1.3 78.7 - - - +
1242G PHE* 1.3 66.6 + - - +
1244G LEU* 3.1 11.9 + - + +
1245G MET* 3.1 43.1 + - + +
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Residues in contact with PHE1242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203G TRP* 5.2 0.2 - + - -
1230G LEU* 6.0 2.2 - - + -
1231G LEU 3.7 17.3 - - - -
1232G ASP* 4.0 1.3 - - - -
1233G LYS* 3.4 66.6 - - + -
1234G PRO* 4.1 2.5 - - + -
1237G CYS* 4.0 8.1 - - - -
1238G PRO 3.5 2.2 + - - +
1239G ASP 3.2 6.1 + - - +
1241G LEU* 1.3 79.1 - - - +
1243G GLU* 1.3 70.4 + - - +
1245G MET* 3.1 23.3 + - + +
1246G ARG* 3.1 51.2 + - + +
1249G TRP* 4.3 13.2 - + - -
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Residues in contact with GLU1243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233G LYS* 5.0 1.4 + - - -
1239G ASP* 2.8 35.9 + - + +
1240G MET* 3.5 7.0 - - - +
1242G PHE* 1.3 87.4 - - - +
1244G LEU* 1.3 61.1 + - - +
1246G ARG* 2.6 37.4 + - - +
1247G MET* 3.3 14.9 + - + +
981H PHE* 3.9 29.2 - - + +
982H SER* 5.0 1.8 - - - -
1041H MET* 3.3 34.2 - - + +
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Residues in contact with LEU1244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113G ILE* 5.4 0.7 - - + -
1116G ALA* 5.2 4.5 - - + -
1198G PHE* 4.6 1.6 - - + -
1202G LEU* 3.6 22.7 - - + -
1240G MET* 3.1 23.0 + - + +
1241G LEU* 3.3 19.3 - - + +
1243G GLU* 1.3 76.2 - - - +
1245G MET* 1.3 65.0 + - - +
1247G MET* 3.4 18.9 + - + +
1248G CYS* 3.3 31.4 + - - -
1257G PRO* 5.1 1.6 - - + -
1262G ILE* 4.3 33.2 - - + -
1265G SER* 5.5 1.8 - - - +
1266G ILE* 5.1 6.7 - - + -
981H PHE* 4.3 17.0 - - + -
986H VAL* 5.6 2.7 - - + -
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Residues in contact with MET1245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199G GLY* 3.9 11.7 - - - +
1202G LEU* 3.7 14.6 - - + +
1203G TRP* 3.6 44.2 - - - +
1206G ALA* 3.9 12.3 - - + -
1234G PRO* 4.8 0.7 - - + -
1237G CYS* 4.0 6.3 - - - -
1241G LEU* 3.1 38.7 + - + +
1242G PHE* 3.1 26.4 + - + +
1244G LEU* 1.3 76.1 - - - +
1246G ARG* 1.3 59.3 + - - +
1248G CYS* 2.8 28.2 + - - +
1249G TRP* 3.0 35.1 + - + -
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Residues in contact with ARG1246 (chain G).
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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1230G LEU* 4.8 19.2 - - + +
1242G PHE* 3.1 51.4 + - + +
1243G GLU* 2.6 36.1 + - - +
1244G LEU 3.4 0.4 - - - -
1245G MET* 1.3 75.1 - - - +
1247G MET* 1.3 61.8 + - - +
1249G TRP* 3.2 18.9 + - + +
1250G GLN* 3.3 17.5 + - - +
1041H MET* 3.5 46.2 - - - +
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Residues in contact with MET1247 (chain G).
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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1243G GLU* 3.3 18.6 - - + +
1244G LEU* 3.5 13.5 - - - +
1246G ARG* 1.3 73.3 - - - +
1248G CYS* 1.3 57.6 + - - +
1249G TRP 3.0 9.8 + - - -
1250G GLN* 3.1 27.0 + - - +
1256G ARG* 3.7 1.0 - - - -
1257G PRO* 3.5 25.2 - - + +
981H PHE* 3.9 15.9 - - + -
982H SER* 3.5 35.2 - - - +
983H ALA 3.6 3.8 - - - +
986H VAL* 3.0 30.7 - - + -
987H TYR* 3.8 19.5 - - + +
1041H MET* 3.5 17.3 - - + -
1045H ILE* 4.4 1.6 - - + -
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Residues in contact with CYS1248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195G VAL* 3.5 31.4 - - + +
1196G TRP* 3.4 14.9 - - - -
1198G PHE* 3.9 28.0 - - - -
1199G GLY* 3.8 14.6 - - - -
1202G LEU* 4.9 0.7 - - - -
1244G LEU* 3.3 27.1 - - - -
1245G MET 2.8 12.2 + - - +
1247G MET* 1.3 74.3 - - - +
1249G TRP* 1.3 57.8 + - - +
1250G GLN 3.5 0.4 - - - -
1256G ARG* 3.2 19.9 + - - -
1257G PRO* 4.1 3.6 - - - -
1262G ILE* 4.1 5.6 - - - -
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Residues in contact with TRP1249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196G TRP* 3.4 59.6 + + + -
1199G GLY* 3.4 28.1 - - - -
1200G VAL* 3.6 6.9 - - + +
1203G TRP* 3.9 11.9 - + + -
1213G TYR* 5.6 1.3 - - - -
1230G LEU* 3.7 34.6 - - + +
1231G LEU* 3.5 56.3 - - + -
1242G PHE* 4.3 8.7 - + - -
1245G MET* 3.0 37.3 + - + +
1246G ARG* 3.2 12.3 + - + +
1247G MET 3.0 1.0 + - - -
1248G CYS* 1.3 85.2 - - + +
1250G GLN* 1.3 68.5 + - - +
1251G TYR* 3.1 3.8 + - - +
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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