Contacts of the strand formed by residues 2121 - 2131 (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 LEU2121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2119C HIS 4.1 0.4 + - - -
2120C ILE* 1.3 84.2 - - - +
2122C VAL* 1.3 68.0 + - - +
2123C THR* 3.7 13.6 + - + +
2141C SER* 3.9 16.6 - - - +
2144C THR 3.3 27.8 - - - +
2145C THR 4.5 0.9 - - - +
2146C LEU* 5.1 1.0 - - - +
2165C ILE* 4.0 21.5 - - + -
2173C PRO* 2.8 15.3 + - - +
2174C SER 3.8 19.3 - - - +
2175C PRO* 3.8 30.1 - - + -
2178C THR* 4.0 6.3 - - + +
2448C SER* 4.4 2.8 + - - -
3114D ILE* 4.2 16.6 - - + -
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Residues in contact with VAL2122 (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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2120C ILE 3.6 0.4 + - - -
2121C LEU* 1.3 73.2 - - - +
2123C THR* 1.3 66.7 + - - +
2141C SER* 3.4 3.3 + - - -
2142C GLN* 3.0 41.0 + - + -
2144C THR* 2.9 20.7 + - + +
2145C THR 3.5 9.6 - - - +
2146C LEU* 3.4 35.7 - - + +
2151C ALA* 3.9 15.3 - - + -
2154C THR* 3.9 8.1 - - - +
2446C TRP* 5.2 0.2 - - + -
2447C THR 3.1 27.6 - - - +
2448C SER* 3.5 8.7 - - - +
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Residues in contact with THR2123 (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* 3.8 10.9 + - + +
2122C VAL* 1.3 81.2 - - - +
2124C ARG* 1.3 72.4 + - - +
2139C ALA* 3.8 23.1 - - + +
2140C LEU 3.2 11.2 - - - -
2141C SER* 4.0 11.0 - - - -
2142C GLN* 4.6 2.5 + - - +
2162C ARG* 4.2 3.1 - - - -
2165C ILE* 4.1 14.1 - - + -
2167C TRP* 5.3 0.7 - - - -
2173C PRO* 4.1 15.1 - - + +
2447C THR 4.0 3.5 - - - +
2448C SER* 3.2 16.5 + - - -
2449C ASN* 2.8 34.0 + - - -
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Residues in contact with ARG2124 (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* 1.3 81.4 - - - +
2125C GLU* 1.3 97.7 + - - +
2126C PRO* 3.4 3.8 - - - -
2139C ALA* 4.0 0.7 - - - +
2140C LEU 3.1 23.6 + - - +
2142C GLN* 5.4 4.5 - - - +
2154C THR 5.9 0.7 - - - +
2155C ILE 6.2 0.4 - - - -
2157C ASP* 4.3 7.5 + - - -
2162C ARG* 3.7 4.9 - - - +
2378C ARG* 4.1 4.4 - - - +
2412C TYR* 3.5 32.9 - - - -
2433C GLU* 2.9 34.9 + - - +
2435C ILE* 3.7 19.5 - - - +
2447C THR* 3.8 28.9 - - + +
2448C SER 4.4 5.6 - - - +
2449C ASN* 3.1 13.0 - - - +
3477C SIA 2.9 23.8 + - - +
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Residues in contact with GLU2125 (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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2124C ARG* 1.3 103.7 + - - +
2126C PRO* 1.4 65.8 - - - +
2127C TYR* 3.7 13.7 - - - -
2139C ALA* 3.9 5.9 - - - -
2140C LEU* 3.8 22.1 + - + +
2157C ASP* 4.2 3.8 - - - +
2162C ARG* 2.9 35.3 + - - -
2234C GLU* 4.2 20.9 - - + +
2412C TYR* 3.9 27.4 - - + -
2433C GLU* 2.8 15.3 + - - -
3477C SIA 3.1 26.7 + - - +
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Residues in contact with PRO2126 (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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2124C ARG 3.4 3.3 - - - -
2125C GLU* 1.4 93.1 - - - +
2127C TYR* 1.3 70.0 + - - +
2138C PHE 3.2 14.8 - - - +
2139C ALA* 4.0 7.6 - - + -
2234C GLU 3.6 0.9 - - - +
2412C TYR* 5.3 1.2 - - + +
2431C TYR* 3.0 28.8 + - + -
2433C GLU* 3.2 34.8 - - + +
2449C ASN* 3.6 16.6 - - - +
2451C ILE* 3.7 27.6 - - + -
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Residues in contact with TYR2127 (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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2125C GLU 3.7 9.2 - - - -
2126C PRO* 1.3 79.0 - - - +
2128C LEU* 1.3 78.9 + - - +
2129C SER* 4.9 0.4 - - - -
2137C MET* 3.5 0.5 - - - +
2138C PHE* 2.8 61.8 + + + +
2164C LEU* 3.4 15.8 - - + +
2187C SER* 2.8 29.2 + - - -
2188C THR* 3.4 19.0 - - - -
2189C SER* 3.6 13.2 + - - -
2234C GLU* 3.3 22.7 - - - -
2235C SER* 3.4 22.9 - - - -
2236C GLU* 3.7 9.4 - - + -
2415C ALA 6.0 0.2 - - - +
2431C TYR* 3.4 26.7 - - + -
2451C ILE* 4.8 0.2 - - - +
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Residues in contact with LEU2128 (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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2127C TYR* 1.3 95.3 - - - +
2129C SER* 1.3 65.3 + - - +
2135C CYS* 5.1 1.8 - - + -
2136C ARG 3.2 9.6 - - - +
2137C MET* 3.7 29.2 - - + -
2138C PHE* 4.5 0.4 - - - -
2169C MET* 3.6 33.4 - - + -
2236C GLU* 3.8 4.0 + - - +
2415C ALA 4.9 0.2 - - - +
2416C PHE* 3.2 55.4 - - + +
2431C TYR* 4.1 12.8 - - + -
2451C ILE* 4.0 22.2 - - + -
2453C ALA* 4.3 8.5 - - + -
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Residues in contact with SER2129 (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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2127C TYR* 4.8 2.7 - - - -
2128C LEU* 1.3 75.3 - - - +
2130C CYS* 1.3 62.0 + - - +
2136C ARG* 2.7 35.4 + - - +
2138C PHE* 3.6 21.7 - - - -
2189C SER 3.7 3.0 + - - -
2190C CYS* 4.0 2.9 - - - -
2191C HIS 4.6 0.2 + - - -
2196C ARG* 3.1 29.4 + - - -
2236C GLU* 2.7 32.0 + - - +
2416C PHE* 4.8 0.2 - - - -
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Residues in contact with CYS2130 (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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2129C SER* 1.3 78.5 + - - +
2131C ASP* 1.3 62.2 + - - +
2134C GLY 3.2 6.7 - - - +
2135C CYS* 2.0 47.8 - - - -
2191C HIS* 3.5 6.9 + - - +
2196C ARG* 3.0 16.0 + - - -
2236C GLU* 3.8 4.7 + - - +
2416C PHE* 4.1 16.2 - - - -
2417C ILE 4.1 4.9 - - - +
2418C ASP* 3.8 30.1 - - - +
2420C TRP* 3.3 19.6 - - + -
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Residues in contact with ASP2131 (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* 3.1 17.2 + - - -
2088C ARG* 5.1 3.7 + - - -
2130C CYS* 1.3 72.7 - - - +
2132C PRO* 1.3 77.7 - - + +
2133C GLN* 2.8 34.3 + - - +
2134C GLY 2.9 19.8 + - - +
2136C ARG* 4.8 13.6 - - - -
2191C HIS* 3.3 27.1 + - + -
2196C ARG* 4.3 6.6 + - - +
2420C TRP* 3.6 15.7 - - - -
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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