Contacts of the strand formed by residues 2102 - 2110 (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 HIS2102 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2097r PRO* 6.0 3.1 - - + +
2100r GLY* 4.9 3.1 - - - -
2101r ALA* 1.3 77.8 - - - +
2103r ASN* 1.3 63.9 + - - +
2123r SER* 3.8 2.6 - - - -
2124r VAL* 3.1 35.7 + - + +
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Residues in contact with ASN2103 (chain r).
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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2070r ASP* 4.9 8.7 - - - +
2102r HIS* 1.3 77.7 - - - +
2104r TYR* 1.3 59.1 + - - +
2122r PHE 3.2 17.9 - - - +
2123r SER* 4.0 10.8 - - - +
2124r VAL* 4.7 1.1 - - - +
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Residues in contact with TYR2104 (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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2068r ILE* 6.0 2.9 - - + -
2069r GLY 3.9 14.6 - - - +
2070r ASP* 4.7 6.7 - - + +
2071r ALA 5.8 0.2 - - - -
2077r ILE* 6.2 2.0 - - + -
2103r ASN* 1.3 75.6 - - - +
2105r THR* 1.3 63.9 + - - +
2121r LYS* 3.5 6.6 - - - +
2122r PHE* 2.9 32.5 + - + +
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Residues in contact with THR2105 (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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2068r ILE* 3.4 5.4 - - - +
2069r GLY 2.9 38.2 + - - -
2071r ALA* 4.9 15.0 - - - -
2104r TYR* 1.3 80.1 - - - +
2106r LEU* 1.3 63.6 + - - +
2107r TYR* 4.0 0.9 + - - +
2119r GLU* 5.9 3.6 - - - -
2120r TYR 3.6 9.2 - - - -
2121r LYS* 4.3 8.5 - - - +
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Residues in contact with LEU2106 (chain r).
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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2067r VAL 3.6 7.0 - - - +
2068r ILE* 4.5 4.5 - - + +
2105r THR* 1.3 74.2 - - - +
2107r TYR* 1.3 60.6 + - - +
2118r GLN 4.3 0.4 - - - -
2119r GLU* 3.3 6.2 - - - +
2120r TYR* 2.9 47.2 + - + +
2122r PHE* 5.3 3.0 - - + +
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Residues in contact with TYR2107 (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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1940r LEU* 6.4 2.9 - - + -
2065r TRP 4.5 0.2 - - - -
2066r VAL* 3.6 4.3 - - - +
2067r VAL* 2.8 47.6 + - + +
2068r ILE 6.3 0.2 - - - -
2105r THR* 4.0 1.5 + - - +
2106r LEU* 1.3 75.6 - - - +
2108r PHE* 1.3 63.1 + - - +
2109r MET* 6.1 1.3 - - + -
2118r GLN 3.3 7.0 - - - +
2119r GLU* 4.7 2.2 - - + +
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Residues in contact with PHE2108 (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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2065r TRP 3.4 7.4 - - - +
2066r VAL* 4.7 3.1 - - + +
2107r TYR* 1.3 77.9 - - - +
2109r MET* 1.3 61.7 + - - +
2116r CYS 5.1 2.9 - - - +
2117r ASP* 3.2 8.9 - - - +
2118r GLN* 2.9 46.8 + - + +
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Residues in contact with MET2109 (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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1940r LEU* 6.5 0.4 - - - -
1943r MET* 4.4 15.0 - - + -
2064r TRP* 3.1 9.7 - - - +
2065r TRP* 2.9 44.9 + - + +
2107r TYR* 5.8 1.6 - - + -
2108r PHE* 1.3 76.9 - - - +
2110r SER* 1.3 64.7 + - - +
2116r CYS 5.6 0.9 - - - -
2117r ASP* 4.7 10.1 - - + +
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Residues in contact with SER2110 (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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1943r MET* 3.7 23.4 - - - +
1947r GLN* 4.6 3.6 - - - +
2062r GLU* 6.3 2.5 - - - -
2063r GLY 3.4 11.0 - - - -
2064r TRP* 5.1 0.7 - - - -
2109r MET* 1.3 76.8 - - - +
2111r ASP* 1.3 60.7 + - - +
2112r ALA* 3.5 10.3 - - - -
2113r TYR* 4.1 23.5 + - - +
2116r CYS* 5.2 11.5 - - - +
2117r ASP* 5.6 3.0 - - - +
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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