Contacts of the strand formed by residues 1265 - 1272 (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 GLN1265 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2270A PHE* 5.7 5.2 - - + -
1228r VAL* 3.5 26.7 + - - +
1263r PRO* 3.2 7.6 - - - +
1264r PRO* 1.3 85.9 - - + +
1266r TYR* 1.3 65.9 + - - +
1283r PRO* 5.3 5.2 - - + -
1284r VAL 3.1 18.2 - - - +
1285r SER* 3.7 9.0 - - - -
1286r PHE* 4.0 4.5 - - - +
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Residues in contact with TYR1266 (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* 5.5 6.1 - - + -
1226r GLU 3.7 12.6 - - - +
1227r ASP* 4.8 5.2 - - - -
1265r GLN* 1.3 78.3 - - - +
1267r PHE* 1.3 64.7 + - - +
1283r PRO* 3.8 2.3 - - - +
1284r VAL* 2.9 38.1 + - + +
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Residues in contact with PHE1267 (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* 3.1 6.2 - - - +
1226r GLU* 2.9 46.5 + - + +
1227r ASP 5.1 2.7 - - - +
1230r SER* 5.9 4.5 - - - -
1266r TYR* 1.3 78.7 - - - +
1268r ILE* 1.3 63.3 + - - +
1269r ARG* 3.9 3.3 + - + +
1281r GLN* 5.9 4.9 - - + -
1282r LEU 3.8 6.7 - - - +
1283r PRO* 5.0 4.3 - - + -
1284r VAL* 5.6 0.7 - - - -
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Residues in contact with ILE1268 (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 4.1 2.7 - - - -
1225r VAL* 4.3 9.4 - - + +
1267r PHE* 1.3 73.4 - - - +
1269r ARG* 1.3 59.5 + - - +
1280r THR 3.9 1.7 - - - +
1281r GLN* 3.7 1.8 - - - -
1282r LEU* 2.9 48.2 + - + +
1284r VAL* 5.1 4.9 - - + +
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Residues in contact with ARG1269 (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 3.7 0.6 - - - +
1223r ILE* 3.3 4.7 - - - +
1224r LEU* 2.9 44.2 + - + +
1226r GLU* 6.0 3.1 - - + -
1267r PHE* 3.9 4.2 - - + +
1268r ILE* 1.3 73.3 - - - +
1270r VAL* 1.3 61.7 + - - +
1271r VAL* 6.2 0.9 - - + -
1280r THR 3.8 4.5 - - - +
1281r GLN* 4.4 9.2 - - + +
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Residues in contact with VAL1270 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1184r LEU* 5.7 8.7 - - + -
1221r PHE* 5.4 6.1 - - + -
1222r TRP 3.3 7.9 - - - +
1223r ILE* 4.6 9.6 - - + -
1268r ILE 4.1 0.2 + - - -
1269r ARG* 1.3 75.2 - - - +
1271r VAL* 1.3 60.0 + - - +
1279r GLU* 3.5 4.4 - - - +
1280r THR* 2.9 47.5 + - - +
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Residues in contact with VAL1271 (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* 3.2 4.5 - - - +
1222r TRP* 2.8 43.7 + - + +
1269r ARG* 5.8 1.6 - - + -
1270r VAL* 1.3 75.4 - - - +
1272r SER* 1.3 67.8 + - - +
1278r CYS 3.8 9.4 - - - +
1279r GLU* 4.6 7.4 - - + -
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Residues in contact with SER1272 (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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1182r PRO* 5.6 6.3 - - - -
1220r ALA 3.2 11.7 - - - -
1221r PHE* 4.1 2.5 - - - +
1271r VAL* 1.3 79.1 - - - +
1273r ASP* 1.3 66.7 + - - +
1274r ARG 4.6 0.7 - - - -
1275r TRP* 3.5 42.0 - - - +
1278r CYS* 3.4 15.9 + - - +
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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