Contacts of the helix formed by residues 2110 - 2116 (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 ASN2110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLY* 4.3 16.5 - - - +
161A PHE* 3.5 43.4 + - - +
162A ARG 5.3 1.8 + - - -
163A ALA* 5.7 3.6 - - - +
183A ILE* 6.0 0.6 - - - +
2108C LYS* 2.7 53.0 + - - +
2109C ASP* 1.3 82.5 + - - +
2111C ALA* 1.3 64.2 + - - +
2112C ILE 3.3 2.6 + - - -
2113C ARG* 3.4 9.1 + - - -
2114C ILE* 3.0 27.1 + - + +
2450C SER* 4.4 5.3 - - - -
2468C ASP 3.9 4.8 - - - +
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Residues in contact with ALA2111 (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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2109C ASP* 3.1 28.6 + - - +
2110C ASN* 1.3 77.2 - - - +
2112C ILE* 1.3 54.9 + - + +
2114C ILE* 3.9 0.5 - - - +
2115C GLY* 2.6 35.2 + - - -
2120C ILE* 4.0 11.6 - - + +
2146C LEU* 4.6 0.2 - - - +
2172C ALA* 3.9 9.0 - - + -
2173C PRO* 4.0 18.8 - - + -
2449C ASN 3.9 17.3 - - - +
2450C SER* 3.7 3.4 - - - -
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Residues in contact with ILE2112 (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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2110C ASN 3.4 0.6 - - - -
2111C ALA* 1.3 74.1 - - + +
2113C ARG* 1.3 66.1 + - - +
2115C GLY 3.7 0.3 - - - -
2116C GLU 3.1 18.0 + - - -
2120C ILE* 6.4 0.2 - - + -
2146C LEU* 3.9 14.8 - - + -
2436C ARG* 3.9 16.6 - - + -
2446C TRP* 4.0 11.2 - - + -
2448C SER* 3.8 16.8 - - - +
2449C ASN 3.6 37.5 - - - +
2450C SER* 4.2 0.8 - - - -
2468C ASP* 3.3 25.8 + - - +
2470C ALA* 3.6 16.8 - - + -
2475C PHE* 3.3 24.9 - - + -
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Residues in contact with ARG2113 (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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142A GLN 3.0 12.1 + - - -
143A GLY 2.9 25.7 + - - +
144A THR* 3.9 15.8 + - - +
145A THR 5.4 0.2 + - - -
150A HIS* 3.3 41.6 + - + +
161A PHE* 3.5 36.5 - - - +
1479A GOL 2.9 44.7 + - - -
2110C ASN* 3.4 11.1 + - + +
2112C ILE* 1.3 78.9 - - - +
2114C ILE* 1.3 62.9 + - - +
2116C GLU* 3.5 6.1 - - - +
2117C ASP* 4.7 0.5 + - - +
2468C ASP* 3.9 10.0 + - - +
2469C GLY 3.0 41.1 + - - +
2470C ALA* 3.7 5.4 - - - +
2471C GLU* 6.2 0.2 - - - +
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Residues in contact with ILE2114 (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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121A LEU* 4.4 14.8 - - + -
143A GLY* 3.8 23.6 - - - +
144A THR* 4.1 7.9 - - - +
145A THR* 4.6 7.7 + - + +
175A PRO* 4.0 20.4 - - + -
2109C ASP 3.4 24.5 - - - +
2110C ASN* 3.0 17.3 + - + +
2111C ALA 3.9 2.5 - - - +
2113C ARG* 1.3 76.6 - - - +
2115C GLY* 1.3 57.8 + - - +
2116C GLU 3.1 2.8 + - - -
2117C ASP* 3.2 4.0 + - - +
2118C ALA* 2.9 41.6 + - + +
2120C ILE* 4.1 13.0 - - + -
2172C ALA* 4.3 10.5 - - + +
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Residues in contact with GLY2115 (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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2111C ALA 2.6 20.3 + - - -
2112C ILE 3.7 2.5 - - - -
2113C ARG 3.4 0.2 - - - -
2114C ILE* 1.3 69.5 - - - +
2116C GLU* 1.3 62.2 + - - +
2117C ASP 3.1 3.5 + - - -
2118C ALA 3.4 10.1 - - - +
2120C ILE* 3.2 28.9 - - - +
2146C LEU* 3.9 18.9 - - - +
2147C ARG* 3.6 13.0 + - - +
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Residues in contact with GLU2116 (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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148A GLY* 3.4 9.9 - - - -
149A ARG* 3.0 47.0 + - - +
150A HIS* 3.7 16.5 + - + +
2112C ILE 3.1 5.1 + - - -
2113C ARG 3.5 15.0 - - - +
2114C ILE 3.1 1.2 - - - -
2115C GLY* 1.3 76.8 - - - +
2117C ASP* 1.3 58.5 + - - +
2147C ARG* 2.8 55.7 + - - +
2474C TYR* 4.3 6.3 - - + -
2475C PHE* 3.5 28.3 - - + -
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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