Contacts of the helix formed by residues 1238 - 1249 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107T PRO 6.0 0.7 - - - +
1109T LEU* 3.9 46.4 - - + +
1112T MET* 4.8 8.7 - - + -
1206T ALA* 5.7 0.2 - - + -
1236T ASN 3.5 8.7 - - - +
1237T CYS* 1.3 94.7 - - - +
1239T ASP* 1.3 65.7 + - - +
1240T MET 3.2 3.2 + - - +
1241T LEU* 3.5 14.0 + - + +
1242T PHE* 3.4 17.0 + - - +
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Residues in contact with ASP1239 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233T LYS* 3.2 24.5 + - - +
1237T CYS 4.0 3.6 - - - +
1238T PRO* 1.3 73.4 - - - +
1240T MET* 1.3 62.4 + - - +
1242T PHE* 3.6 2.4 + - - +
1243T GLU* 3.2 29.9 + - - +
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Residues in contact with MET1240 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981I PHE* 3.7 45.2 - - + +
1109T LEU* 3.9 25.4 - - + -
1113T ILE* 3.2 37.7 - - + -
1238T PRO* 3.2 1.7 - - + -
1239T ASP* 1.3 76.0 - - - +
1241T LEU* 1.3 61.9 + - + +
1243T GLU* 2.6 27.8 + - - +
1244T LEU* 2.9 23.5 + - + +
1266T ILE* 3.6 27.6 - - + -
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Residues in contact with LEU1241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109T LEU* 4.8 2.9 - - + -
1112T MET* 3.4 49.8 - - + -
1113T ILE* 3.8 27.1 - - + -
1116T ALA* 5.0 2.0 - - + -
1202T LEU* 4.1 27.6 - - + +
1205T ILE* 5.7 0.9 - - + -
1206T ALA* 4.2 10.5 - - + -
1237T CYS* 4.2 4.9 - - - -
1238T PRO* 3.5 20.7 + - + +
1240T MET* 1.3 83.5 - - + +
1242T PHE* 1.3 59.8 + - - +
1244T LEU* 3.5 10.2 - - + +
1245T MET* 3.3 31.6 + - + +
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Residues in contact with PHE1242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230T LEU* 6.4 1.8 - - + -
1231T LEU 3.7 17.3 - - - -
1232T ASP* 4.0 2.0 - - - -
1233T LYS* 3.4 59.5 - - + -
1234T PRO* 3.8 3.1 - - + -
1237T CYS* 4.0 14.3 - - - -
1238T PRO 3.4 5.0 + - - +
1239T ASP 4.0 5.8 - - - +
1240T MET 3.1 1.0 - - - -
1241T LEU* 1.3 76.5 - - - +
1243T GLU* 1.3 68.5 + - - +
1244T LEU 3.2 0.4 - - - -
1245T MET* 3.4 20.4 + - - -
1246T ARG* 3.1 53.2 + - + +
1249T TRP* 4.1 12.8 - + - -
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Residues in contact with GLU1243 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981I PHE* 4.4 18.6 - - + +
982I SER* 4.8 3.8 - - - -
1041I MET* 3.5 12.8 - - + +
1233T LYS* 5.5 1.7 + - - -
1239T ASP* 3.2 20.5 + - - +
1240T MET* 2.6 20.2 + - - +
1242T PHE* 1.3 78.4 - - - +
1244T LEU* 1.3 64.3 + - - +
1246T ARG* 2.6 44.9 + - - +
1247T MET* 3.3 34.9 + - + +
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Residues in contact with LEU1244 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981I PHE* 4.1 19.0 - - + -
986I VAL* 4.8 3.6 - - + -
1116T ALA* 5.4 5.2 - - + -
1198T PHE* 5.0 0.4 - - + -
1202T LEU* 3.7 20.9 - - + -
1240T MET* 2.9 26.3 + - + +
1241T LEU* 3.5 16.4 - - + +
1243T GLU* 1.3 72.5 - - - +
1245T MET* 1.3 67.4 + - - +
1247T MET* 2.8 37.0 + - + +
1248T CYS* 3.0 15.3 + - - -
1257T PRO* 5.2 0.4 - - + -
1262T ILE* 4.2 41.7 - - + -
1265T SER* 5.1 0.4 - - - +
1266T ILE* 4.9 7.0 - - + -
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Residues in contact with MET1245 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199T GLY* 3.8 11.9 - - - +
1202T LEU* 3.5 19.2 - - + +
1203T TRP* 3.3 37.7 - - + +
1206T ALA* 4.1 14.4 - - + -
1234T PRO* 4.7 0.4 - - + -
1237T CYS* 4.4 4.9 - - - -
1241T LEU* 3.3 24.4 + - + +
1242T PHE* 3.5 23.3 - - - +
1244T LEU* 1.3 76.0 - - - +
1246T ARG* 1.3 57.4 + - - +
1248T CYS* 2.7 30.3 + - - +
1249T TRP* 2.8 50.3 + - + -
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Residues in contact with ARG1246 (chain T).
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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1040I SER* 5.8 0.8 - - - +
1041I MET* 3.7 40.5 - - - +
1230T LEU* 5.5 14.1 - - + +
1242T PHE* 3.1 42.0 + - + +
1243T GLU* 2.6 47.3 + - - +
1245T MET* 1.3 79.3 - - - +
1247T MET* 1.3 61.1 + - - +
1249T TRP* 3.6 12.5 + - + +
1250T GLN* 3.5 24.8 + - - +
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Residues in contact with MET1247 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981I PHE* 3.2 36.1 - - + -
982I SER 3.8 17.3 - - - -
983I ALA* 3.9 4.7 - - - +
986I VAL* 3.5 24.2 - - - -
987I TYR* 3.8 28.7 - - + +
1041I MET* 3.6 20.6 - - + -
1045I ILE* 4.6 1.3 - - + -
1243T GLU* 3.3 23.6 - - + +
1244T LEU* 2.8 15.7 + - + +
1246T ARG* 1.3 72.3 - - - +
1248T CYS* 1.3 63.7 + - - +
1249T TRP 3.0 2.7 + - - -
1250T GLN* 3.2 21.7 + - - +
1256T ARG* 3.6 1.2 - - - +
1257T PRO* 3.3 21.4 - - + +
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Residues in contact with CYS1248 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195T VAL* 3.6 26.2 - - - +
1196T TRP* 3.4 13.9 - - - -
1198T PHE* 3.7 20.2 - - - -
1199T GLY* 3.7 16.4 - - - -
1202T LEU* 4.9 0.7 - - - -
1244T LEU* 3.0 18.9 + - - +
1245T MET* 2.7 7.9 + - - +
1247T MET* 1.3 75.9 - - - +
1249T TRP* 1.3 57.9 + - + +
1250T GLN 3.4 1.1 - - - -
1256T ARG* 3.2 21.2 + - - -
1257T PRO* 4.2 2.7 - - - -
1262T ILE* 3.7 30.1 - - - -
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Residues in contact with TRP1249 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196T TRP* 3.4 58.7 + + + -
1199T GLY* 3.3 25.5 - - - -
1200T VAL* 3.5 12.1 - - + +
1203T TRP* 4.0 2.5 - + + -
1213T TYR* 5.9 0.9 - - - -
1230T LEU* 3.7 35.1 - - + +
1231T LEU* 3.8 52.0 - - + -
1242T PHE* 4.1 9.2 - + - -
1245T MET* 2.8 50.4 + - + +
1246T ARG* 3.6 12.5 + - + +
1247T MET 3.0 0.6 - - - -
1248T CYS* 1.3 85.3 - - + +
1250T GLN* 1.3 67.2 + - - +
1251T TYR* 3.1 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