Contacts of the strand formed by residues 2144 - 2155 (chain A) in PDB entry 5W0P
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 CYS2144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.3 11.7 - - - +
145A ASN* 6.0 0.2 - - + -
146A PHE* 3.2 31.1 - - + -
2066A PHE* 4.4 13.7 - - - -
2067A ARG* 3.4 15.3 - - - -
2068A TYR* 3.9 16.4 - - + -
2069A GLY 4.6 0.9 - - - +
2132A MET* 3.8 5.9 - - - +
2133A LEU* 3.2 47.2 + - + +
2143A SER* 1.3 75.0 + - - +
2145A GLY* 1.3 62.7 + - - +
2324A ILE* 5.1 0.2 - - - -
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Residues in contact with GLY2145 (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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2066A PHE* 5.3 0.9 - - - -
2067A ARG* 2.8 42.2 + - - +
2131A VAL 3.3 10.1 - - - -
2132A MET* 3.8 8.7 - - - -
2144A CYS* 1.3 77.0 - - - +
2146A VAL* 1.3 65.2 + - - -
2147A ASP* 4.0 1.3 + - - +
2324A ILE* 4.1 10.1 - - - -
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Residues in contact with VAL2146 (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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2064A CYS* 4.3 12.1 - - - -
2065A ALA 3.8 11.2 - - - +
2066A PHE* 3.5 36.1 - - + +
2084A LEU* 4.0 17.9 - - + -
2128A PRO* 4.3 5.6 - - + -
2129A CYS 4.1 19.5 - - - +
2130A SER* 4.0 3.8 - - - -
2131A VAL* 2.6 30.5 + - + +
2132A MET* 5.3 1.2 - - - +
2145A GLY* 1.3 73.0 - - - -
2147A ASP* 1.3 67.9 + - - +
2148A PHE* 4.7 2.5 - - + -
2323A GLY* 4.4 1.8 - - - -
2324A ILE* 3.8 22.4 - - + +
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Residues in contact with ASP2147 (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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2063A THR 3.9 0.9 - - - +
2064A CYS* 3.9 0.9 - - - -
2065A ALA* 3.2 35.3 + - - +
2067A ARG* 3.0 44.4 + - - -
2130A SER* 4.9 4.3 - - - -
2145A GLY 4.1 4.8 - - - +
2146A VAL* 1.3 81.0 - - - +
2148A PHE* 1.3 70.9 + - - +
2149A GLU* 5.4 1.7 - - - +
2174A LEU* 3.7 18.7 - - + +
2175A ILE 5.3 1.1 - - - +
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Residues in contact with PHE2148 (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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2062A LEU* 5.2 3.6 - - + -
2063A THR 3.4 4.9 - - - +
2064A CYS* 3.5 39.3 - - + -
2123A PHE* 3.9 17.9 - + - -
2127A LEU* 4.0 17.9 - - + -
2128A PRO 3.4 24.2 - - - -
2129A CYS 4.1 9.0 - - - -
2130A SER* 3.3 21.3 - - - -
2146A VAL* 4.7 2.9 - - + -
2147A ASP* 1.3 77.8 - - - +
2149A GLU* 1.3 62.8 + - - +
2174A LEU* 3.7 9.6 - - - +
2175A ILE* 3.1 50.4 + - + +
2176A ARG* 5.1 0.2 - - - -
2177A LYS* 3.6 30.7 - - + -
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Residues in contact with GLU2149 (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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2062A LEU* 5.2 0.6 - - - +
2063A THR* 2.7 55.1 + - + +
2067A ARG* 4.5 14.4 + - - +
2081A ARG* 5.5 5.2 + - - -
2147A ASP* 5.4 2.0 - - - +
2148A PHE* 1.3 75.9 - - - +
2150A VAL* 1.3 62.6 + - - +
2151A LYS* 3.5 29.5 + - + +
2172A ARG* 3.3 41.3 + - + +
2173A LEU 3.8 8.3 - - - +
2174A LEU* 3.6 25.0 - - + +
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Residues in contact with VAL2150 (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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2025A ILE* 3.9 25.7 - - + +
2027A LEU* 4.2 12.1 - - + -
2042A VAL* 4.0 15.7 - - + -
2060A VAL* 4.3 4.0 - - + -
2061A THR 3.6 13.2 - - - +
2062A LEU* 4.0 12.8 - - + -
2119A PHE* 4.6 1.6 - - + -
2121A LEU* 4.2 11.2 - - + -
2149A GLU* 1.3 71.9 - - - +
2151A LYS* 1.3 62.0 + - - +
2172A ARG* 3.5 1.0 - - - -
2173A LEU* 2.9 37.9 + - - +
2175A ILE* 3.5 36.1 - - + -
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Residues in contact with LYS2151 (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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2025A ILE* 4.7 1.3 - - - -
2060A VAL* 3.4 7.5 - - - +
2061A THR* 2.7 50.4 + - + +
2063A THR* 3.9 17.2 - - + +
2081A ARG* 5.8 4.0 - - - +
2149A GLU* 3.5 28.4 + - + +
2150A VAL* 1.3 77.7 - - - +
2152A ALA* 1.3 61.1 + - - +
2153A PHE* 5.4 2.7 - - + -
2162A GLU* 4.4 13.8 + - - +
2165A ILE* 4.4 21.9 - - - +
2170A SER* 5.8 4.3 - - - -
2171A VAL 3.4 7.9 - - - +
2172A ARG* 3.7 28.8 - - + +
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Residues in contact with ALA2152 (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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2023A VAL* 4.1 12.8 - - + -
2025A ILE* 4.0 19.3 - - + -
2046A VAL* 4.7 7.0 - - + -
2059A TYR 3.4 13.7 - - - +
2060A VAL* 4.6 4.0 - - + -
2151A LYS* 1.3 77.0 - - - +
2153A PHE* 1.3 62.2 + - - +
2169A SER 4.0 0.2 - - - +
2170A SER* 3.4 0.5 - - - -
2171A VAL* 2.7 57.7 + - + +
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Residues in contact with PHE2153 (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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2023A VAL* 4.3 7.2 - - - +
2058A VAL* 3.3 3.9 - - - +
2059A TYR* 2.9 69.4 + + + -
2061A THR* 3.8 16.8 - - + -
2088A ARG* 4.3 8.1 - - - -
2151A LYS* 5.1 3.1 - - + -
2152A ALA* 1.3 81.8 - - - +
2154A ALA* 1.3 63.0 + - - +
2155A SER* 4.0 20.4 - - - -
2161A GLU 4.6 4.9 - - - -
2162A GLU* 3.7 25.4 - - - -
2165A ILE* 3.8 33.9 - - + -
2166A PRO 5.1 0.7 - - - +
2169A SER* 3.9 9.4 - - - +
2170A SER* 3.7 22.2 - - - +
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Residues in contact with ALA2154 (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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2022A SER* 5.0 0.7 - - - +
2023A VAL* 3.9 18.1 - - + +
2053A VAL* 4.2 17.7 - - + -
2056A LYS* 4.8 9.0 - - + -
2057A LYS 3.5 5.4 - - - +
2058A VAL* 4.1 14.1 - - + +
2153A PHE* 1.3 75.7 - - - +
2155A SER* 1.3 62.1 + - - +
2166A PRO* 3.7 8.5 - - - +
2169A SER* 2.8 36.6 + - - -
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Residues in contact with SER2155 (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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2056A LYS* 4.4 4.6 - - - +
2057A LYS* 2.9 37.9 + - - +
2059A TYR* 5.5 1.1 - - - -
2153A PHE* 4.0 22.0 - - - -
2154A ALA* 1.3 75.4 - - - +
2156A ASP* 1.3 66.9 + - - +
2157A ILE* 3.2 28.6 + - - +
2161A GLU* 5.9 1.1 - - - +
2164A LYS 5.8 0.3 + - - -
2165A ILE* 5.5 1.2 - - - +
2166A PRO* 4.4 16.2 - - - +
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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