Contacts of the strand formed by residues 1233 - 1242 (chain r) 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 ILE1233 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100r LEU 5.7 1.1 - - - +
1103r GLY* 2.9 33.6 + - - +
1105r ALA* 4.3 10.0 - - + +
1224r LEU* 5.3 9.0 - - + -
1225r VAL 3.7 7.4 - - - +
1226r GLU* 4.3 3.6 - - + +
1232r VAL* 1.3 73.1 - - - +
1234r LEU* 1.3 65.2 + - - +
1235r HIS* 3.3 8.8 - - - +
1236r HIS* 5.6 2.7 - - + -
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Residues in contact with LEU1234 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225r VAL* 2.8 18.0 + - + +
1226r GLU 5.2 0.9 - - - -
1227r ASP* 5.1 10.1 - - + +
1232r VAL* 3.5 6.5 + - - -
1233r ILE* 1.3 72.7 - - - +
1235r HIS* 1.3 63.6 + - + +
1256r VAL* 5.0 15.7 - - + -
1257r PRO* 5.6 8.5 - - + +
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Residues in contact with HIS1235 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224r LEU* 3.3 3.6 - - - +
1225r VAL* 2.8 37.9 + - + +
1233r ILE* 3.3 4.1 - - - -
1234r LEU* 1.3 83.7 - - + +
1236r HIS* 1.3 62.0 + - - +
1254r PHE* 5.9 5.8 - - + -
1255r PHE 4.7 13.9 - - - +
1256r VAL* 5.4 5.2 - - + -
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Residues in contact with HIS1236 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222r TRP* 6.3 1.3 - - + -
1223r ILE 3.3 11.2 - - - +
1224r LEU* 3.6 13.2 - - + -
1233r ILE* 5.6 4.3 - - + -
1235r HIS* 1.3 77.1 - - - +
1237r GLU* 1.3 61.3 - - - +
1709r SER* 5.0 10.9 + - - -
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Residues in contact with GLU1237 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222r TRP* 3.6 4.2 - - - +
1223r ILE* 2.9 39.6 + - + +
1236r HIS* 1.3 75.7 - - - +
1238r TYR* 1.3 64.0 + - - +
1239r PHE* 3.7 3.1 + - + +
1709r SER* 5.0 14.4 - - - -
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Residues in contact with TYR1238 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221r PHE 3.9 4.9 - - - +
1222r TRP* 4.8 2.5 - - - +
1237r GLU* 1.3 73.8 - - - +
1239r PHE* 1.3 59.8 + - - +
1240r LEU* 4.1 2.2 + - - +
1533r SER* 4.6 24.0 - - - -
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Residues in contact with PHE1239 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220r ALA* 4.0 0.5 - - - +
1221r PHE* 2.7 52.7 + - + +
1223r ILE* 5.2 10.5 - - + -
1237r GLU* 3.7 6.5 + - + +
1238r TYR* 1.3 72.2 - - - +
1240r LEU* 1.3 61.6 + - - +
1241r LEU 4.2 0.9 + - - -
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Residues in contact with LEU1240 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218r SER* 5.9 5.2 - - - -
1219r GLU 3.7 7.4 - - - +
1220r ALA* 4.6 7.2 - - + +
1238r TYR 4.1 2.4 + - - +
1239r PHE* 1.3 76.3 - - - +
1241r LEU* 1.3 61.8 + - - +
1242r LYS* 3.8 2.9 + - - +
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Residues in contact with LEU1241 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218r SER* 4.8 0.9 - - - -
1219r GLU* 3.0 38.8 + - + +
1239r PHE 4.2 1.0 + - - -
1240r LEU* 1.3 71.5 - - - +
1242r LYS* 1.3 67.7 + - - +
1245r TYR* 5.6 8.1 - - + +
1246r ALA* 5.8 2.5 - - - +
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Residues in contact with LYS1242 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217r SER 3.8 8.3 - - - +
1218r SER* 4.4 6.7 - - - +
1240r LEU 3.8 4.5 + - - +
1241r LEU* 1.3 78.6 - - - +
1243r ALA* 1.3 67.9 + - - +
1244r LYS* 3.4 7.6 - - + +
1245r TYR* 3.6 17.0 + - + +
1246r ALA* 3.7 9.2 + - - +
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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