Contacts of the helix formed by residues 2101 - 2115 (chain C) in PDB entry 1G24
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 PRO2101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2089C LYS* 4.4 16.2 - - - +
2099C GLY 3.8 1.8 - - - +
2100C PHE* 1.3 92.5 - - + +
2102C SER* 1.3 66.0 + - - +
2103C ASN* 4.5 5.8 - - + +
2104C LEU* 2.9 30.6 + - + +
2105C ILE* 3.1 7.8 + - - +
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Residues in contact with SER2102 (chain C).
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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2100C PHE 3.5 3.4 + - - -
2101C PRO* 1.3 71.6 - - - +
2103C ASN* 1.3 64.8 + - - +
2105C ILE* 3.3 13.3 + - - +
2106C LYS* 3.1 22.0 + - - +
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Residues in contact with ASN2103 (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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2101C PRO* 3.2 3.9 - - + +
2102C SER* 1.3 79.4 - - - +
2104C LEU* 1.3 61.8 + - - +
2106C LYS* 3.4 15.4 + - - +
2107C GLN* 3.1 33.2 + - - +
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Residues in contact with LEU2104 (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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2086C ILE* 4.1 28.5 - - + -
2089C LYS* 3.8 29.8 - - + +
2100C PHE* 3.7 30.7 - - + -
2101C PRO* 2.9 23.6 + - + +
2103C ASN* 1.3 76.0 - - - +
2105C ILE* 1.3 67.3 + - - +
2107C GLN* 3.2 20.0 + - + +
2108C VAL* 2.8 38.1 + - + +
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Residues in contact with ILE2105 (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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2097C ILE* 3.4 34.3 - - + +
2098C ASN* 3.7 14.4 - - - +
2100C PHE* 3.4 22.7 - - + +
2101C PRO 3.1 10.5 + - - +
2102C SER* 3.6 14.4 - - - +
2104C LEU* 1.3 73.8 - - - +
2106C LYS* 1.3 64.3 + - - +
2108C VAL* 3.3 5.5 + - - +
2109C GLU* 2.9 54.0 + - + +
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Residues in contact with LYS2106 (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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2102C SER 3.1 13.2 + - - +
2103C ASN* 3.4 18.6 + - - +
2105C ILE* 1.3 79.5 - - - +
2107C GLN* 1.3 62.9 + - + +
2109C GLU* 3.4 5.6 + - - +
2110C LEU* 3.0 43.2 + - + +
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Residues in contact with GLN2107 (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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2075C ALA* 3.8 19.9 - - + +
2078C SER* 3.1 34.8 + - - -
2086C ILE* 4.9 6.5 - - + +
2103C ASN* 3.1 19.3 + - + +
2104C LEU* 3.7 25.6 - - + +
2106C LYS* 1.3 74.2 - - + +
2108C VAL* 1.3 61.5 + - - +
2110C LEU* 3.2 6.6 + - + +
2111C LEU* 2.9 37.6 + - + +
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Residues in contact with VAL2108 (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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2086C ILE* 4.7 13.5 - - + -
2090C LEU* 5.0 1.8 - - + -
2097C ILE* 4.1 14.6 - - + -
2100C PHE* 4.5 13.5 - - + -
2104C LEU* 2.8 38.1 + - + +
2105C ILE 3.8 3.4 - - - +
2107C GLN* 1.3 76.5 - - + +
2109C GLU* 1.3 59.2 + - - +
2111C LEU* 3.2 4.1 + - + -
2112C ASP* 2.8 47.2 + - - +
2172C TYR* 3.3 21.5 + - + +
2219C ARG* 3.5 20.0 - - - +
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Residues in contact with GLU2109 (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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2097C ILE* 3.9 23.1 - - + +
2105C ILE* 2.9 36.1 + - - +
2106C LYS* 4.0 5.0 - - - +
2108C VAL* 1.3 75.5 - - - +
2110C LEU* 1.3 62.2 + - - +
2112C ASP* 3.7 10.2 - - - +
2113C LYS* 3.1 25.1 + - - +
2250C PRO* 5.4 0.3 - - - +
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Residues in contact with LEU2110 (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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2069C SER* 5.1 0.7 - - - +
2071C SER* 3.8 39.3 - - - +
2072C GLU* 4.2 21.6 - - + +
2075C ALA* 3.9 13.7 - - + -
2106C LYS* 3.0 40.3 + - + +
2107C GLN* 3.5 7.4 - - + +
2109C GLU* 1.3 76.2 - - + +
2111C LEU* 1.3 59.7 + - - +
2113C LYS* 3.3 4.5 + - + +
2114C SER* 2.8 30.8 + - - -
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Residues in contact with LEU2111 (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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2072C GLU 5.9 0.2 - - - -
2075C ALA* 3.5 33.0 - - + +
2076C ILE* 3.6 22.2 - - + +
2079C TYR* 4.1 23.6 - - + -
2086C ILE* 5.2 5.8 - - + -
2107C GLN* 2.9 23.9 + - + +
2108C VAL* 4.3 5.6 - - + -
2110C LEU* 1.3 76.5 - - - +
2112C ASP* 1.3 63.7 + - - +
2114C SER* 2.6 24.3 + - - +
2115C PHE* 3.3 12.5 - - + -
2172C TYR* 3.6 38.8 - - + +
2216C LEU* 5.0 8.7 - - + -
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Residues in contact with ASP2112 (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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2108C VAL* 2.8 28.9 + - - +
2109C GLU* 3.7 11.8 - - - +
2111C LEU* 1.3 75.5 - - - +
2113C LYS* 1.3 60.1 + - - +
2115C PHE* 3.5 21.9 + - - +
2116C ASN* 4.7 1.6 + - - +
2172C TYR* 2.8 25.8 + - - -
2199C LYS* 5.2 0.9 + - - -
2218C PRO* 6.1 0.8 - - - +
2219C ARG* 3.0 38.8 + - - +
2248C ILE* 3.5 26.5 - - + +
2250C PRO* 4.0 15.0 - - + +
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Residues in contact with LYS2113 (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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2072C GLU* 4.3 11.0 + - - +
2109C GLU 3.1 15.8 + - - +
2110C LEU* 4.0 4.3 - - + +
2112C ASP* 1.3 75.7 - - - +
2114C SER* 1.3 65.8 + - - +
2115C PHE 3.0 2.5 - - - -
2116C ASN* 3.0 35.6 + - - +
2117C LYS* 4.4 5.3 + - - +
2250C PRO* 3.8 19.5 - - + +
2251C LYS 3.9 26.7 - - - -
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Residues in contact with SER2114 (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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2068C LEU* 4.2 7.7 - - - +
2072C GLU* 3.6 28.9 + - - -
2076C ILE* 4.5 8.9 - - - +
2110C LEU 2.8 15.4 + - - -
2111C LEU* 2.6 24.3 + - - +
2113C LYS* 1.3 76.4 - - - +
2115C PHE* 1.3 63.6 + - - +
2116C ASN 3.1 0.2 - - - -
2117C LYS* 3.0 18.2 + - - +
2118C MET* 3.2 30.4 + - - +
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Residues in contact with PHE2115 (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 LEU* 3.3 26.9 - - + -
2112C ASP* 3.7 12.1 - - - +
2113C LYS 3.0 1.4 - - - -
2114C SER* 1.3 76.1 + - - +
2116C ASN* 1.3 57.6 + - - +
2117C LYS 2.9 7.1 + - - -
2118C MET* 3.1 28.5 + - + +
2119C LYS* 2.9 18.9 + - - -
2172C TYR* 4.3 13.7 - + - -
2199C LYS* 3.7 30.7 - - + +
2200C ALA* 4.0 7.4 - - - -
2201C GLY 4.0 6.5 - - - -
2216C LEU* 3.2 42.2 - - + -
2217C LEU 3.7 6.5 - - - -
2218C PRO* 3.5 46.2 - - + -
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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