Contacts of the helix formed by residues 1226 - 1238 (chain A) in PDB entry 3F2B
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 GLU1226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1224A GLY 3.8 1.6 + - - -
1225A LEU* 1.3 70.2 - - - +
1227A PRO* 1.3 89.0 - - - +
1228A SER* 4.1 20.0 + - - +
1229A LEU* 2.9 26.7 + - + +
1230A ALA* 2.9 10.1 + - - +
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Residues in contact with PRO1227 (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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966A PHE* 3.3 41.7 - - + -
1221A ILE* 3.8 30.1 - - + -
1225A LEU 3.5 4.0 - - - +
1226A GLU* 1.3 99.1 - - - +
1228A SER* 1.3 57.6 + - - +
1230A ALA* 3.0 4.0 + - - +
1231A PHE 2.7 26.2 + - - -
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Residues in contact with SER1228 (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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966A PHE* 3.7 26.1 - - - -
967A LYS* 3.9 30.3 + - - -
1226A GLU* 3.2 14.8 + - - +
1227A PRO* 1.3 78.9 - - - +
1229A LEU* 1.3 61.7 + - - +
1231A PHE* 3.4 7.0 + - - +
1232A LYS* 3.0 34.7 + - - +
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Residues in contact with LEU1229 (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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1225A LEU* 3.8 21.1 - - + -
1226A GLU* 2.9 19.5 + - + +
1228A SER* 1.3 81.0 + - - +
1230A ALA* 1.3 64.6 + - - +
1231A PHE 3.1 0.2 - - - -
1232A LYS* 3.1 23.1 + - - +
1233A ILE* 3.1 28.0 + - + +
1247A PHE* 3.9 33.2 - - + -
1250A GLU* 3.7 39.5 - - + +
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Residues in contact with ALA1230 (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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1217A MET* 3.7 30.3 - - + +
1220A LEU* 3.7 24.2 - - + +
1221A ILE* 3.8 15.3 - - + +
1225A LEU* 4.7 3.5 - - + +
1226A GLU 2.9 10.4 + - - +
1227A PRO 3.0 7.6 + - - +
1229A LEU* 1.3 77.6 - - - +
1231A PHE* 1.3 58.2 + - - +
1233A ILE* 3.4 5.9 + - - +
1234A MET* 3.0 27.7 + - - +
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Residues in contact with PHE1231 (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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961A GLU 3.4 25.1 - - - -
962A THR 4.6 1.6 - - - -
965A GLY* 3.5 20.6 - - - -
966A PHE* 3.9 7.6 - + + -
969A ASP 6.4 0.2 - - - -
970A LYS* 3.8 26.9 - - + -
1217A MET* 2.8 29.6 - - + +
1227A PRO 2.7 7.4 + - - +
1228A SER* 3.5 11.7 - - - +
1229A LEU 3.1 0.2 - - - -
1230A ALA* 1.3 76.0 - - - +
1232A LYS* 1.3 75.5 + - + +
1234A MET* 3.3 23.6 + - + +
1235A GLU* 2.9 52.0 + - + +
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Residues in contact with LYS1232 (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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1228A SER* 3.0 17.1 + - - +
1229A LEU* 3.5 36.3 - - - +
1231A PHE* 1.3 86.4 - - + +
1233A ILE* 1.3 57.6 + - - +
1235A GLU* 3.3 6.3 + - - +
1236A SER* 2.9 28.4 + - - -
1247A PHE* 4.3 24.4 - - + -
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Residues in contact with ILE1233 (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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1216A ILE* 4.3 3.4 - - + -
1220A LEU* 3.6 21.1 - - + -
1225A LEU* 4.0 26.2 - - + -
1229A LEU* 3.1 23.6 + - + +
1230A ALA 3.8 4.3 - - - +
1231A PHE 3.0 0.6 - - - -
1232A LYS* 1.3 74.3 - - - +
1234A MET* 1.3 65.1 + - - +
1236A SER* 3.3 2.4 + - - -
1237A VAL* 2.8 35.4 + - + +
1243A LEU* 4.0 18.8 - - + -
1247A PHE* 3.5 49.6 - - + -
1251A MET* 4.1 13.0 - - + -
1264A CYS* 5.5 0.2 - - - -
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Residues in contact with MET1234 (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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962A THR* 4.1 23.8 - - + -
1213A ARG* 3.0 49.1 - - + +
1214A ASP* 3.9 4.9 - - - -
1216A ILE* 4.1 12.2 - - - +
1217A MET* 3.7 24.2 - - + +
1230A ALA 3.0 14.5 + - - +
1231A PHE* 3.4 34.8 - - + +
1233A ILE* 1.3 79.0 - - - +
1235A GLU* 1.3 82.2 + - - +
1237A VAL* 3.2 3.0 + - - +
1238A ARG* 3.1 23.6 + - - +
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Residues in contact with GLU1235 (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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962A THR 5.0 0.6 - - - +
970A LYS* 3.3 21.7 + - - +
1213A ARG* 4.0 4.2 + - - -
1231A PHE* 2.9 50.3 + - + +
1232A LYS* 3.6 6.7 - - - +
1234A MET* 1.3 89.1 - - + +
1236A SER* 1.3 62.3 + - - +
1238A ARG* 2.8 47.5 + - - +
1239A LYS* 3.2 42.3 + - - +
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Residues in contact with SER1236 (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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1232A LYS 2.9 16.9 + - - -
1233A ILE 3.3 4.2 + - - -
1235A GLU* 1.3 76.8 - - - +
1237A VAL* 1.3 60.7 + - - +
1239A LYS* 3.3 9.1 + - - +
1241A LYS* 2.8 43.9 + - - +
1242A GLY 2.5 27.0 + - - -
1244A THR* 6.0 0.7 - - - +
1247A PHE* 4.0 17.6 - - - -
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Residues in contact with VAL1237 (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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1216A ILE* 3.4 31.6 - - + -
1233A ILE* 2.8 38.5 + - + +
1234A MET 4.0 0.4 - - - +
1236A SER* 1.3 77.0 - - - +
1238A ARG* 1.3 61.5 + - - +
1239A LYS 3.1 0.2 - - - -
1240A GLY* 2.9 20.6 + - - -
1242A GLY 4.3 8.7 - - - +
1243A LEU* 4.3 6.5 - - + -
1264A CYS* 3.8 31.0 - - + +
1267A ILE* 3.4 33.5 - - + +
1270A MET* 4.8 0.9 - - + -
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Residues in contact with ARG1238 (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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970A LYS* 3.9 3.6 - - - +
1213A ARG* 3.3 53.6 - - + +
1234A MET 3.1 20.8 + - - +
1235A GLU* 2.8 45.6 + - - +
1237A VAL* 1.3 77.9 - - + +
1239A LYS* 1.3 80.2 + - - +
1240A GLY 3.2 1.6 - - - -
1269A TYR* 3.6 16.2 - - - -
1270A MET* 3.4 42.9 + - + +
1456A DGT 3.3 32.1 + - - -
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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