Contacts of the strand formed by residues 2134 - 2145 (chain C) in PDB entry 1W21
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 GLY2134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A GLY 5.8 2.7 - - - -
217A ARG* 3.7 15.6 - - - +
2130C CYS* 3.2 2.1 - - - +
2131C ASP* 2.9 36.4 + - - +
2132C PRO 3.5 0.2 - - - -
2133C GLN* 1.3 80.7 - - - +
2135C CYS* 1.3 64.4 + - - -
2136C ARG* 5.7 1.3 - - - +
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Residues in contact with CYS2135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 6.5 0.4 - - - -
2106C LEU* 5.7 3.4 - - - -
2128C LEU* 5.1 2.9 - - + -
2129C SER 3.6 4.5 - - - +
2130C CYS* 2.0 44.4 - - - -
2134C GLY* 1.3 75.7 - - - -
2136C ARG* 1.3 70.3 + - - +
2168C GLU* 5.0 1.6 - - - +
2169C MET* 3.4 44.3 + - + +
2416C PHE* 5.0 5.2 - - + -
2418C ASP* 4.1 16.8 - - - -
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Residues in contact with ARG2136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2128C LEU* 3.2 8.1 - - - +
2129C SER 2.7 35.0 + - - +
2131C ASP* 4.8 13.7 - - - -
2134C GLY 5.7 1.3 - - - -
2135C CYS* 1.3 79.3 - - - +
2137C MET* 1.3 66.5 + - - +
2138C PHE* 3.6 17.3 - - + -
2166C SER* 2.7 44.1 + - - -
2167C TRP* 3.4 13.9 - - - +
2168C GLU* 3.8 21.4 - - + +
2169C MET* 4.1 1.1 - - - +
2177C ASN 5.4 1.2 + - - -
2179C ARG* 3.6 42.3 - - - +
2181C GLU* 5.0 0.2 + - - -
2196C ARG* 5.6 6.0 - - - +
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Residues in contact with MET2137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2107C SER* 3.3 33.7 - - - +
2108C LYS 4.4 4.3 - - - +
2109C ASP* 4.0 14.4 - - + +
2127C TYR 3.5 6.5 - - - +
2128C LEU* 3.7 21.5 - - + -
2136C ARG* 1.3 72.7 - - - +
2138C PHE* 1.3 62.2 - - - +
2166C SER* 3.2 4.3 - - - -
2167C TRP* 2.9 66.2 + - + +
2169C MET* 3.9 7.1 - - + +
2170C GLY 3.5 16.2 - - - +
2171C GLN 3.9 4.5 - - - +
2451C ILE* 3.9 33.9 - - + -
2453C ALA* 5.5 0.7 - - + -
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Residues in contact with PHE2138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126C PRO* 3.2 3.7 - - - +
2127C TYR* 2.8 65.9 + + + +
2129C SER* 3.6 26.5 - - - -
2136C ARG* 3.6 30.7 - - + -
2137C MET* 1.3 78.1 - - - +
2139C ALA* 1.3 64.5 + - - +
2164C LEU* 4.1 10.5 - - + -
2165C ILE 3.2 6.7 - - - -
2166C SER* 3.7 22.7 - - - -
2167C TRP* 3.8 4.9 - - - -
2181C GLU* 3.9 15.3 - - + -
2189C SER* 3.6 17.5 - - - -
2196C ARG* 3.7 27.1 - - - -
2451C ILE* 4.5 0.5 - - - +
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Residues in contact with ALA2139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2123C THR* 3.8 22.0 - - + +
2124C ARG 4.0 1.6 - - - +
2125C GLU 3.9 9.4 - - - -
2126C PRO* 4.0 13.7 - - + -
2138C PHE* 1.3 77.8 - - - +
2140C LEU* 1.3 63.2 + - - +
2141C SER 3.7 0.2 - - - -
2164C LEU* 3.5 8.0 - - - +
2165C ILE* 2.9 35.7 + - - +
2167C TRP* 3.6 20.6 - - + -
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Residues in contact with LEU2140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2123C THR* 3.2 16.0 - - - -
2124C ARG 3.1 10.1 + - - +
2125C GLU* 3.8 23.3 + - + +
2139C ALA* 1.3 73.9 - - - +
2141C SER* 1.3 60.4 + - - +
2162C ARG* 2.9 37.1 + - - +
2163C ALA 3.4 1.3 - - - +
2164C LEU* 3.9 25.8 - - + +
2184C GLY 3.7 20.4 - - - +
2185C TRP* 3.3 29.8 - - - +
2186C SER* 3.8 9.0 - - - +
2187C SER* 4.2 16.6 - - - +
2200C CYS* 5.1 0.2 - - - -
2234C GLU* 3.9 12.3 - - - +
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Residues in contact with SER2141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121C LEU* 3.9 17.6 - - - +
2122C VAL 3.4 11.5 + - - -
2123C THR* 4.0 3.6 - - - -
2139C ALA 3.5 3.8 + - - -
2140C LEU* 1.3 77.5 - - - +
2142C GLN* 1.3 61.7 + - - +
2143C GLY* 3.0 15.2 + - - -
2161C PHE 5.4 0.2 - - - -
2162C ARG* 3.2 28.5 + - - +
2163C ALA* 2.9 19.0 + - - -
2165C ILE* 4.0 25.7 - - - +
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Residues in contact with GLN2142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2122C VAL* 3.0 37.2 + - + +
2123C THR* 4.6 3.0 + - - +
2124C ARG* 5.4 3.6 - - - +
2141C SER* 1.3 75.9 + - - +
2143C GLY* 1.3 58.9 + - - +
2144C THR* 3.4 1.6 - - + -
2154C THR* 3.1 44.9 + - + -
2156C HIS 3.2 17.7 + - - +
2159C SER* 4.4 0.5 + - - -
2161C PHE* 3.4 8.9 - - - +
2162C ARG* 3.3 38.4 - - - +
2447C THR 5.3 0.6 + - - -
3479C GOL 2.9 35.1 + - - +
3113D ARG* 3.1 13.5 + - - -
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Residues in contact with GLY2143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2141C SER* 3.0 12.5 + - - -
2142C GLN* 1.3 79.0 - - - +
2144C THR* 1.3 59.1 + - - +
2161C PHE 3.3 15.1 + - - -
3110D ASN* 4.4 9.1 - - - +
3113D ARG* 2.8 36.6 + - - +
3114D ILE* 3.8 16.7 - - - +
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Residues in contact with THR2144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121C LEU* 3.3 13.6 - - - +
2122C VAL* 2.9 38.1 + - + +
2142C GLN* 4.1 4.9 - - + +
2143C GLY* 1.3 80.0 - - - +
2145C THR* 1.4 72.9 + - - +
2148C GLY* 4.5 2.8 - - - -
2150C HIS* 3.3 47.4 + - - +
2151C ALA* 3.3 12.0 + - - +
2154C THR* 4.1 4.7 - - + -
3113D ARG* 3.9 8.3 + - - +
3114D ILE* 3.9 12.7 - - - +
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Residues in contact with THR2145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2118C ALA 5.6 0.4 - - - -
2119C HIS* 4.1 18.4 - - + -
2120C ILE 3.2 16.4 - - - +
2121C LEU* 4.6 1.3 - - + -
2122C VAL* 3.6 1.8 - - - -
2144C THR* 1.4 87.7 + - - +
2146C LEU* 1.3 64.8 + - - +
2147C ARG* 4.2 1.3 - - - -
2148C GLY* 3.1 17.0 + - - -
2151C ALA* 3.4 8.8 - - - +
2175C PRO* 4.2 12.3 - - + -
3113D ARG 5.4 0.2 + - - -
3114D ILE* 4.7 7.8 + - + +
3117D ASP* 3.0 27.7 + - - +
3118D ALA* 4.1 26.0 - - + -
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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