Contacts of the strand formed by residues 2125 - 2132 (chain A) 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 ALA2125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2124A ILE* 1.3 81.3 - - - +
2126A GLY* 1.3 58.9 + - - +
2146A VAL 4.8 0.7 - - - +
2147A MET* 5.0 7.1 - - - +
2148A VAL 5.1 2.4 + - - -
2157A VAL* 4.3 17.9 - - + +
2177A TRP* 6.3 0.7 - - + -
2178A ILE 3.4 11.2 - - - +
2179A HIS* 4.2 8.7 - - + +
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Residues in contact with GLY2126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2125A ALA* 1.3 77.0 - - - +
2127A TYR* 1.3 65.6 + - - -
2128A LEU* 4.9 0.2 - - - +
2145A ILE* 5.7 3.1 - - - -
2146A VAL 3.4 12.1 - - - -
2147A MET* 5.1 0.9 - - - -
2148A VAL 5.7 0.4 - - - -
2177A TRP* 3.4 4.2 - - - +
2178A ILE* 2.9 37.6 + - - +
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Residues in contact with TYR2127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126A GLY* 1.3 74.2 - - - -
2128A LEU* 1.3 62.1 + - - +
2129A TYR* 6.4 0.4 - - + -
2144A CYS 3.6 0.6 - - - +
2145A ILE* 3.3 7.4 - - - +
2146A VAL* 2.8 49.2 + - + +
2148A VAL* 6.2 0.6 - - - +
2176A GLY 4.9 0.4 - - - +
2177A TRP* 3.7 12.1 - - + -
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Residues in contact with LEU2128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126A GLY 3.8 0.9 + - - +
2127A TYR* 1.3 76.3 - - - +
2129A TYR* 1.3 61.4 + - - +
2142A ILE* 4.9 13.5 - - + -
2144A CYS 3.6 4.7 - - - +
2145A ILE* 5.0 0.2 - - - +
2174A PRO* 4.0 3.6 - - - +
2175A LEU* 3.3 24.0 + - + +
2176A GLY 3.1 31.0 + - - +
2177A TRP* 4.1 6.1 - - - +
2178A ILE* 5.0 3.1 - - + +
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Residues in contact with TYR2129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2127A TYR* 4.3 0.4 - - + -
2128A LEU* 1.3 75.6 - - - +
2130A GLY* 1.3 60.1 + - - +
2142A ILE* 3.5 5.8 - - - +
2143A ARG 2.9 19.9 + - - -
2144A CYS* 3.1 28.8 + - + +
2169A LEU* 5.6 5.2 - - + +
2172A MET* 4.0 14.8 - - + -
2173A GLU 3.6 13.5 - - - +
2174A PRO* 5.2 0.9 - - + -
2175A LEU* 4.7 0.9 - - - +
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Residues in contact with GLY2130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2129A TYR* 1.3 77.2 - - - +
2131A VAL* 1.3 61.8 + - - -
2140A LYS* 6.1 1.3 - - - -
2141A GLU 3.0 16.2 - - - -
2142A ILE* 3.8 2.7 - - - -
2143A ARG* 3.7 6.1 - - - -
2172A MET* 3.3 9.6 - - - +
2173A GLU* 3.1 31.6 + - - +
2175A LEU* 4.9 5.7 - - - +
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Residues in contact with VAL2131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2130A GLY* 1.3 74.8 - - - -
2132A SER* 1.3 65.8 + - - +
2140A LYS* 3.7 6.6 - - - +
2141A GLU* 2.9 34.8 + - + +
2143A ARG* 5.4 2.8 - - + +
2171A GLU 5.2 8.5 - - - +
2172A MET* 5.2 2.2 - - + +
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Residues in contact with SER2132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2131A VAL* 1.3 81.6 - - - +
2133A PRO* 1.3 69.9 - - - +
2134A PRO 3.9 0.2 - - - -
2136A ASN 4.2 10.1 - - - -
2137A PRO* 4.5 13.2 - - - -
2139A VAL 4.4 8.1 - - - -
2140A LYS* 5.5 0.9 - - - -
2141A GLU* 5.8 1.1 - - - -
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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