Contacts of the strand formed by residues 2057 - 2068 (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 LYS2057 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2055A GLY 5.1 5.9 + - - -
2056A LYS* 1.3 76.2 - - - +
2058A VAL* 1.3 63.4 + - - +
2059A TYR* 3.6 40.1 - - + +
2090A GLN* 4.7 10.8 - - - +
2092A TYR 3.5 5.2 - - - +
2093A PRO* 4.9 1.1 - - + -
2154A ALA* 3.5 1.7 - - - -
2155A SER 2.9 35.1 + - - +
2156A ASP 3.4 11.9 + - - -
2157A ILE 3.7 13.9 - - - +
2158A THR* 4.0 15.3 - - - +
-20B GLN 5.8 0.9 - - - -
-19B THR* 5.7 1.3 - - - +
-18B PRO* 3.7 29.7 - - + +
-17B ASN* 2.5 36.6 + - - -
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Residues in contact with VAL2058 (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* 4.4 10.5 - - + -
2046A VAL* 4.4 9.6 - - + -
2048A VAL* 3.8 29.6 - - + -
2053A VAL* 3.7 28.0 - - + -
2057A LYS* 1.3 71.8 - - - +
2059A TYR* 1.3 71.5 + - - +
2090A GLN* 4.0 1.4 - - - +
2091A VAL* 3.1 35.2 + - + -
2092A TYR* 2.8 30.6 + - + +
2153A PHE 3.3 11.0 - - - +
2154A ALA* 4.1 7.9 - - + -
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Residues in contact with TYR2059 (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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2057A LYS* 3.6 44.9 - - + +
2058A VAL* 1.3 78.0 - - - +
2060A VAL* 1.3 59.8 + - - +
2088A ARG* 3.9 18.2 - - - +
2089A VAL 3.7 16.4 - - - +
2090A GLN* 3.8 31.4 + - + -
2091A VAL* 3.8 4.8 - - - +
2152A ALA* 3.4 7.1 - - - +
2153A PHE* 2.9 63.4 + + + +
2155A SER* 5.5 0.9 - - - -
2157A ILE 4.6 5.6 - - - -
2158A THR 4.6 0.7 - - - -
2159A ASP* 3.3 49.4 + - - +
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Residues in contact with VAL2060 (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 1.1 - - + -
2046A VAL* 5.1 1.1 - - + -
2059A TYR* 1.3 75.3 - - - +
2061A THR* 1.3 70.2 + - - +
2088A ARG* 3.7 5.5 - - - -
2089A VAL* 3.2 45.1 + - + +
2091A VAL* 3.6 17.5 - - + -
2119A PHE* 3.7 46.4 - - + -
2121A LEU* 4.0 12.6 - - + +
2150A VAL* 4.3 4.9 - - + -
2151A LYS 3.4 12.6 - - - +
2152A ALA* 4.6 6.7 - - + -
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Residues in contact with THR2061 (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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2060A VAL* 1.3 78.6 - - - +
2062A LEU* 1.3 60.2 + - - +
2063A THR* 3.4 11.7 + - - -
2086A PHE* 3.8 17.2 - - + -
2087A SER 3.4 9.9 - - - -
2088A ARG* 3.7 17.9 - - - -
2121A LEU* 3.5 17.5 - - - +
2150A VAL* 3.6 4.9 - - - +
2151A LYS* 2.7 49.6 + - + +
2153A PHE* 3.8 24.2 - - + -
2162A GLU* 4.1 5.2 - - - +
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Residues in contact with LEU2062 (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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2042A VAL* 3.8 18.6 - - + -
2061A THR* 1.3 74.4 - - - +
2063A THR* 1.3 63.0 + - - +
2064A CYS* 3.9 1.0 + - + +
2085A TYR* 3.8 15.7 - - + +
2086A PHE* 3.4 7.7 - - - -
2087A SER* 3.2 36.8 + - - -
2121A LEU* 3.9 21.8 - - + +
2122A THR 3.5 25.6 - - - +
2123A PHE* 3.6 36.8 - - + -
2148A PHE* 5.2 5.2 - - + -
2149A GLU 3.9 2.0 - - - +
2150A VAL* 4.0 15.0 - - + -
2175A ILE* 4.1 4.5 - - + -
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Residues in contact with THR2063 (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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2061A THR* 3.4 17.8 + - - -
2062A LEU* 1.3 72.0 - - - +
2064A CYS* 1.3 61.1 + - - +
2065A ALA* 3.9 11.8 + - + +
2081A ARG* 5.1 5.6 - - - +
2083A ASP* 3.9 21.8 - - - +
2085A TYR 3.9 2.9 - - - +
2086A PHE* 3.4 22.2 - - + -
2147A ASP 3.9 0.5 - - - +
2148A PHE* 3.4 4.9 - - - -
2149A GLU* 2.7 57.8 + - + +
2151A LYS* 3.9 10.7 - - + +
2162A GLU* 5.1 0.2 + - - -
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Residues in contact with CYS2064 (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* 3.9 1.8 + - + +
2063A THR* 1.3 71.5 - - - +
2065A ALA* 1.3 61.2 + - - +
2083A ASP* 3.7 1.4 - - - -
2084A LEU* 2.8 51.1 + - - +
2085A TYR* 3.0 30.2 + - + +
2127A LEU* 4.6 5.4 - - + -
2128A PRO* 4.6 7.0 - - - -
2146A VAL* 4.3 6.1 - - - -
2147A ASP 3.9 3.6 - - - -
2148A PHE* 3.5 43.1 - - + -
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Residues in contact with ALA2065 (chain A).
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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2063A THR* 3.8 8.9 - - + +
2064A CYS* 1.3 74.3 - - - +
2066A PHE* 1.3 61.4 + - - +
2067A ARG* 3.5 6.0 + - - +
2081A ARG* 3.3 37.2 - - - +
2082A ARG 4.1 4.3 - - - +
2083A ASP* 3.8 5.2 - - - +
2084A LEU* 4.3 4.3 - - - +
2146A VAL* 3.8 1.0 - - - +
2147A ASP* 3.2 42.4 + - - +
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Residues in contact with PHE2066 (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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142A PRO* 3.9 25.1 - - + -
2065A ALA* 1.3 70.1 - - - +
2067A ARG* 1.3 71.1 + - - +
2068A TYR* 4.0 14.2 - + - -
2081A ARG* 3.6 17.2 - - - +
2082A ARG 3.2 22.9 + - - +
2084A LEU* 3.8 19.8 - - + +
2133A LEU* 6.4 0.2 - - + -
2144A CYS* 4.4 6.1 - - - -
2145A GLY 4.4 1.8 - - - -
2146A VAL* 3.5 16.8 - - + +
2248A VAL* 3.8 19.5 - - + -
2249A VAL 4.6 3.1 - - - -
2250A LEU* 4.1 19.1 - - + -
2323A GLY* 3.6 25.8 - - - -
2324A ILE* 3.6 35.7 - - + -
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Residues in contact with ARG2067 (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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2065A ALA* 3.5 6.4 + - - +
2066A PHE* 1.3 76.2 - - - +
2068A TYR* 1.3 62.3 + - - +
2069A GLY 5.0 7.0 - - - +
2071A GLU* 3.5 26.3 + - - +
2081A ARG* 4.4 25.4 - - + +
2143A SER* 5.2 11.4 - - - +
2144A CYS* 3.4 6.1 - - - -
2145A GLY 2.8 46.5 + - - +
2147A ASP* 3.0 36.1 + - - +
2149A GLU* 4.5 20.4 + - - +
2172A ARG* 6.3 0.2 - - - -
2174A LEU* 4.9 5.7 - - - +
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Residues in contact with TYR2068 (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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138A VAL 4.4 2.2 - - - -
139A VAL* 4.0 27.6 - - + +
142A PRO* 3.8 25.6 - - + +
145A ASN* 3.5 21.3 - - - +
2066A PHE* 4.0 18.8 - + + -
2067A ARG* 1.3 79.3 - - - +
2069A GLY* 1.3 59.0 + - - +
2070A GLN 4.6 0.7 - - - +
2074A ASP* 2.7 42.4 - - + +
2079A THR* 5.1 1.2 - - - +
2080A PHE 3.8 16.8 + - - -
2081A ARG* 4.0 26.2 - - + +
2082A ARG 4.3 3.1 - - - -
2143A SER 3.6 4.5 - - - -
2144A CYS* 3.9 8.7 - - - -
2250A LEU* 3.7 18.4 - - + -
2251A TYR* 3.9 17.3 + - - -
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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