Contacts of the helix formed by residues 1230 - 1245 (chain U) in PDB entry 6FF7
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 TYR1230 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1196U TYR 5.9 0.7 - - - +
1198U TYR* 3.9 33.9 - - + +
1228U THR* 3.3 6.7 - - - -
1229U THR* 1.3 82.1 - - - +
1231U ASN* 1.3 64.2 + - - +
1232U GLY 4.3 1.3 - - - +
1233U GLN* 3.2 9.4 + - + +
1234U LYS* 3.1 19.5 + - - +
1259U THR* 5.1 3.5 - - - -
1276U VAL* 5.0 8.2 - - + +
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Residues in contact with ASN1231 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230U TYR* 1.3 71.1 - - - +
1232U GLY* 1.3 65.6 + - - +
1234U LYS* 3.1 10.5 + - + +
1235U HIS* 3.1 24.3 + - - +
1259U THR* 5.2 6.9 - - - -
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Residues in contact with GLY1232 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196U TYR 5.7 0.2 + - - -
1197U PHE* 3.9 25.2 - - - +
1198U TYR 3.3 15.3 + - - +
1199U GLN* 4.4 4.3 - - - +
1230U TYR* 3.2 2.4 - - - +
1231U ASN* 1.3 78.8 - - - +
1233U GLN* 1.3 58.4 + - - +
1235U HIS* 3.6 5.7 + - - +
1236U LEU* 3.3 21.3 + - - +
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Residues in contact with GLN1233 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198U TYR 3.0 13.9 + - - +
1199U GLN* 4.4 10.3 - - - +
1200U ASN 4.9 3.1 - - - +
1204U ALA* 5.3 4.4 - - + +
1228U THR* 4.3 16.4 - - - -
1230U TYR* 3.2 13.1 + - + +
1231U ASN 3.2 0.4 - - - -
1232U GLY* 1.3 74.3 - - - +
1234U LYS* 1.3 59.7 + - - +
1236U LEU* 3.2 7.3 + - - +
1237U ILE* 2.9 31.6 + - - +
1274U SER* 5.6 4.9 - - - -
1276U VAL* 4.7 11.2 - - + -
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Residues in contact with LYS1234 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228U THR* 4.8 6.2 - - - -
1230U TYR 3.1 12.1 + - - +
1231U ASN* 3.1 15.8 + - + +
1233U GLN* 1.3 78.3 - - - +
1235U HIS* 1.3 62.3 + - - +
1237U ILE* 3.4 5.5 + - - +
1238U ARG* 3.0 23.0 + - - +
1257U VAL* 4.9 9.7 - - - +
1258U THR* 4.7 25.1 - - - +
1259U THR* 4.9 2.0 - - - +
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Residues in contact with HIS1235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231U ASN 3.1 11.5 + - - +
1232U GLY* 4.0 5.4 - - - +
1234U LYS* 1.3 78.2 - - - +
1236U LEU* 1.3 57.0 + - - +
1238U ARG* 3.5 8.3 + - - +
1239U ASP* 2.8 28.3 + - - +
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Residues in contact with LEU1236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199U GLN* 4.6 12.1 - - + -
1200U ASN 5.9 0.7 - - - +
1204U ALA* 4.9 11.5 - - + +
1232U GLY 3.3 15.2 + - - +
1233U GLN* 3.2 8.9 + - - +
1234U LYS 3.2 0.6 - - - -
1235U HIS* 1.3 77.1 - - - +
1237U ILE* 1.3 60.3 + - - +
1239U ASP* 3.2 9.7 + - - +
1240U ILE* 3.0 27.5 + - - +
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Residues in contact with ILE1237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204U ALA* 4.6 18.3 - - + +
1207U VAL* 6.0 3.6 - - + -
1208U VAL* 5.3 4.6 - - + +
1226U ILE* 5.9 6.1 - - + -
1233U GLN 2.9 16.5 + - - +
1234U LYS* 3.8 6.3 - - - +
1236U LEU* 1.3 75.5 - - - +
1238U ARG* 1.3 57.5 + - - +
1240U ILE* 3.2 7.4 + - - +
1241U ILE* 2.8 29.2 + - - +
1257U VAL* 5.5 6.7 - - + -
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Residues in contact with ARG1238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234U LYS 3.0 14.5 + - - +
1235U HIS* 3.5 12.3 - - - +
1237U ILE* 1.3 77.2 - - - +
1239U ASP* 1.3 62.3 + - - +
1241U ILE* 3.1 9.0 + - - +
1242U ASN* 3.1 23.9 + - - +
1257U VAL* 5.1 13.5 - - + +
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Residues in contact with ASP1239 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235U HIS 2.8 19.6 + - - +
1236U LEU* 3.2 11.0 + - - +
1238U ARG* 1.3 75.3 - - - +
1240U ILE* 1.3 57.7 + - - +
1242U ASN* 3.5 5.3 + - - +
1243U ARG* 3.1 29.0 + - - +
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Residues in contact with ILE1240 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204U ALA* 5.4 8.3 - - + +
1205U GLU* 5.6 3.4 - - - -
1208U VAL* 4.7 16.4 - - + -
1236U LEU 3.0 15.3 + - - +
1237U ILE* 3.7 7.0 - - - +
1239U ASP* 1.3 74.9 - - - +
1241U ILE* 1.3 60.3 + - - +
1243U ARG* 4.4 4.7 - - - +
1244U ARG* 2.9 38.7 + - + +
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Residues in contact with ILE1241 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208U VAL* 5.2 6.0 - - + +
1237U ILE 2.8 15.1 + - - +
1238U ARG* 3.4 13.5 - - - +
1240U ILE* 1.3 76.3 - - - +
1242U ASN* 1.3 57.3 + - - +
1245U CYS* 3.0 39.0 + - + +
1246U GLY 3.4 0.2 + - - -
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Residues in contact with ASN1242 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238U ARG 3.1 14.8 + - - +
1239U ASP* 3.9 5.2 - - - +
1241U ILE* 1.3 76.8 - - - +
1243U ARG* 1.3 58.7 + - - +
1244U ARG 3.4 0.2 - - - -
1246U GLY* 3.2 25.8 - - - +
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Residues in contact with ARG1243 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1239U ASP 3.1 18.9 + - - +
1240U ILE* 3.3 4.5 + - - +
1242U ASN* 1.3 77.2 - - - +
1244U ARG* 1.3 58.6 + - - +
1246U GLY* 5.0 0.4 - - - -
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Residues in contact with ARG1244 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208U VAL* 5.9 4.9 - - + -
1240U ILE* 2.9 17.6 + - + +
1241U ILE* 5.3 0.2 - - - -
1243U ARG* 1.3 79.6 - - - +
1245U CYS* 1.3 64.8 + - - +
1248U ASN* 5.3 1.0 - - - +
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Residues in contact with CYS1245 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241U ILE* 3.0 18.1 + - + +
1244U ARG* 1.3 80.9 - - - +
1246U GLY* 1.3 67.1 + - - +
1247U ASN 3.1 3.6 + - - -
1248U ASN* 3.2 23.8 + - + +
1251U ILE* 4.5 20.6 - - + +
1252U GLY 4.9 8.7 - - - +
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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