Contacts of the helix formed by residues 1238 - 1249 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106A PRO* 5.0 6.7 - - + -
1107A PRO 5.9 0.9 - - - +
1109A LEU* 4.0 42.0 - - + +
1112A MET* 5.2 9.0 - - - -
1236A ASN 3.3 10.3 - - - +
1237A CYS* 1.3 90.3 - - + +
1239A ASP* 1.3 68.7 + - - +
1240A MET* 3.0 4.9 + - + +
1241A LEU* 3.0 11.3 + - + +
1242A PHE 3.5 4.9 + - - -
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Residues in contact with ASP1239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233A LYS* 2.8 31.3 + - - +
1237A CYS 3.1 4.2 + - - -
1238A PRO* 1.3 69.0 - - - +
1240A MET* 1.3 65.7 + - - +
1242A PHE* 2.8 16.0 + - - +
1243A GLU* 2.8 35.3 + - + +
980B SER* 6.5 1.1 - - - -
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Residues in contact with MET1240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A LEU* 4.2 21.8 - - + -
1113A ILE* 3.7 33.2 - - + -
1238A PRO* 3.0 3.4 + - + +
1239A ASP* 1.3 76.5 - - - +
1241A LEU* 1.3 66.3 + - - +
1243A GLU* 3.0 16.4 + - - +
1244A LEU* 3.1 25.8 + - + +
1266A ILE* 3.8 21.5 - - + -
981B PHE* 3.4 53.2 - - + -
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Residues in contact with LEU1241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A LEU* 4.4 11.2 - - + -
1112A MET* 3.6 42.2 - - + -
1113A ILE* 3.8 27.8 - - + -
1116A ALA* 4.9 3.4 - - + -
1202A LEU* 4.0 31.8 - - + +
1205A ILE* 5.2 1.6 - - + -
1206A ALA* 4.4 1.1 - - + -
1237A CYS* 4.3 5.2 - - - -
1238A PRO* 3.0 12.5 + - + +
1240A MET* 1.3 84.2 - - + +
1242A PHE* 1.3 58.4 + - - +
1244A LEU* 3.5 7.8 - - + +
1245A MET* 3.2 43.2 + - + +
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Residues in contact with PHE1242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230A LEU* 6.1 1.8 - - + -
1231A LEU 3.8 16.4 - - - -
1232A ASP* 3.9 2.5 - - - -
1233A LYS* 3.4 59.9 - - + -
1234A PRO* 4.0 2.9 - - + -
1237A CYS* 4.3 13.2 - - - -
1238A PRO 3.5 3.1 + - - +
1239A ASP* 2.8 9.6 + - - +
1241A LEU* 1.3 79.6 - - - +
1243A GLU* 1.3 71.6 + - - +
1244A LEU 3.3 0.2 - - - -
1245A MET* 3.5 19.7 + - - +
1246A ARG* 3.1 48.8 + - + +
1249A TRP* 4.1 13.9 - + - -
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Residues in contact with GLU1243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1239A ASP* 2.8 36.8 + - + +
1240A MET* 3.4 8.7 - - - +
1242A PHE* 1.3 83.5 - - - +
1244A LEU* 1.3 65.0 + - - +
1246A ARG* 3.0 32.9 + - - +
1247A MET* 3.1 32.3 + - + +
981B PHE* 3.7 25.6 - - + +
982B SER* 5.3 0.6 - - - -
1041B MET* 3.1 23.2 - - - +
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Residues in contact with LEU1244 (chain A).
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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1113A ILE* 5.5 0.2 - - + -
1116A ALA* 5.3 2.2 - - + -
1198A PHE* 4.8 1.3 - - + -
1202A LEU* 3.9 18.8 - - + -
1240A MET* 3.1 30.2 + - + +
1241A LEU* 3.5 17.3 - - + +
1243A GLU* 1.3 78.8 - - - +
1245A MET* 1.3 62.4 + - - +
1247A MET* 3.2 19.2 + - - +
1248A CYS* 3.1 33.7 + - - -
1257A PRO* 5.1 2.2 - - + -
1262A ILE* 4.3 33.4 - - + -
1265A SER* 5.2 1.8 - - - +
1266A ILE* 4.8 11.4 - - + -
981B PHE* 4.5 9.4 - - + -
986B VAL* 5.7 2.7 - - + -
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Residues in contact with MET1245 (chain A).
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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1199A GLY* 3.9 4.7 - - - +
1202A LEU* 3.7 42.6 - - + +
1203A TRP* 3.8 29.8 - - + -
1206A ALA* 4.0 3.1 - - + -
1234A PRO* 4.8 0.7 - - + -
1237A CYS* 3.9 20.0 - - - -
1241A LEU* 3.2 32.0 + - + +
1242A PHE* 3.7 23.6 - - + +
1243A GLU 3.2 0.6 - - - -
1244A LEU* 1.3 76.1 - - - +
1246A ARG* 1.3 64.2 + - - +
1248A CYS* 2.9 18.4 + - - +
1249A TRP* 2.9 37.8 + - + -
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Residues in contact with ARG1246 (chain A).
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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1230A LEU* 4.8 18.4 - - + +
1242A PHE* 3.1 49.0 + - + +
1243A GLU* 3.0 34.5 + - - +
1245A MET* 1.3 76.8 - - - +
1247A MET* 1.3 59.5 + - - +
1249A TRP* 3.5 16.3 + - + +
1250A GLN* 3.1 19.3 + - - +
1041B MET* 3.5 39.9 - - + +
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Residues in contact with MET1247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243A GLU* 3.2 22.0 - - + +
1244A LEU* 3.6 12.1 - - - +
1245A MET 3.1 0.6 - - - -
1246A ARG* 1.3 74.3 - - - +
1248A CYS* 1.3 61.1 + - - +
1249A TRP 3.0 5.6 + - - -
1250A GLN* 3.3 19.1 + - - +
1256A ARG* 3.6 6.1 - - - +
1257A PRO* 3.3 20.6 - - + +
981B PHE* 3.5 30.1 - - + -
982B SER 3.7 22.2 - - - +
983B ALA* 3.9 2.9 - - - +
986B VAL* 3.1 27.8 - - - -
987B TYR* 3.6 25.5 + - + +
1041B MET* 3.6 20.0 - - + -
1045B ILE* 4.8 0.4 - - + -
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Residues in contact with CYS1248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195A VAL* 3.6 31.0 - - + +
1196A TRP* 3.4 15.2 + - - -
1198A PHE* 4.0 19.7 - - - -
1199A GLY* 3.9 13.9 - - - -
1202A LEU* 5.1 0.7 - - - -
1244A LEU* 3.1 31.2 + - - -
1245A MET 2.9 7.9 + - - +
1247A MET* 1.3 76.7 - - - +
1249A TRP* 1.3 59.3 + - - +
1250A GLN 3.4 0.2 - - - -
1256A ARG* 3.4 18.3 + - - -
1257A PRO* 4.0 7.9 - - - -
1262A ILE* 4.0 5.8 - - - -
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Residues in contact with TRP1249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196A TRP* 3.3 57.3 + + + -
1199A GLY* 3.5 29.6 - - - -
1200A VAL* 3.6 8.9 - - + +
1203A TRP* 3.8 11.9 - + + -
1213A TYR* 5.8 0.9 - - - -
1230A LEU* 3.9 33.3 - - + +
1231A LEU* 3.6 54.5 - - + -
1242A PHE* 4.1 9.9 - + - -
1245A MET* 2.9 35.7 + - + +
1246A ARG* 3.5 12.5 + - + +
1247A MET 3.0 0.4 - - - -
1248A CYS* 1.3 87.3 - - + +
1250A GLN* 1.3 68.1 + - - +
1251A TYR* 3.2 3.3 + - - -
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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