Contacts of the helix formed by residues 2198 - 2208 (chain C) in PDB entry 1Y1S
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 GLU2198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2067C THR* 4.5 0.9 - - - +
2068C GLY 4.0 7.9 - - - +
2069C ILE* 3.7 9.4 - - - +
2070C GLY 3.1 25.5 + - - +
2071C GLY* 4.8 4.5 - - - +
2074C THR* 3.2 30.5 - - + +
2091C ARG* 2.7 52.5 + - + +
2158C SER* 3.9 0.9 - - - -
2196C GLU* 2.9 3.3 + - - +
2197C MET* 1.3 90.2 + - - +
2199C SER* 1.3 68.6 + - - +
2200C ALA 3.4 2.7 - - - -
2201C THR* 3.4 6.7 + - - +
2202C LEU* 3.0 22.6 + - - +
7002C SO4 4.1 7.7 + - - -
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Residues in contact with SER2199 (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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2091C ARG* 5.1 1.1 - - - +
2110C THR* 5.0 0.9 - - - -
2113C SER* 2.9 25.7 + - - -
2156C THR* 4.1 2.4 - - - +
2158C SER* 3.6 2.4 - - - -
2196C GLU* 2.6 37.5 + - - +
2198C GLU* 1.3 75.6 - - - +
2200C ALA* 1.3 58.0 + - - -
2202C LEU* 3.0 7.7 + - - -
2203C LEU* 2.7 46.3 + - - +
2215C MET* 3.6 21.5 - - - -
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Residues in contact with ALA2200 (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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2113C SER* 4.1 9.6 - - - -
2114C VAL 4.2 0.7 - - - +
2115C ARG* 4.0 16.4 - - + -
2117C ASP* 3.7 22.9 - - - +
2120C SER* 2.9 5.8 + - - +
2130C ALA* 4.3 3.8 - - - -
2158C SER* 3.0 31.8 + - - +
2199C SER* 1.3 77.8 + - - +
2201C THR* 1.3 58.8 + - - +
2204C THR* 2.7 33.1 + - - -
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Residues in contact with THR2201 (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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2071C GLY* 3.4 33.4 - - - +
2074C THR* 4.8 2.5 - - - -
2075C SER* 4.1 14.6 - - - +
2117C ASP* 2.5 25.8 + - - +
2119C ALA* 3.2 30.3 - - + +
2120C SER* 3.9 4.7 - - - +
2123C PHE* 4.8 3.4 - - + -
2158C SER* 4.5 0.2 + - - -
2197C MET 5.6 0.2 + - - -
2198C GLU* 3.4 7.3 + - - -
2199C SER 3.1 0.4 - - - -
2200C ALA* 1.3 76.3 - - - +
2202C LEU* 1.3 64.8 + - - +
2204C THR* 4.2 0.5 - - - -
2205C MET* 3.1 29.1 + - - +
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Residues in contact with LEU2202 (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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2024C VAL* 4.9 4.3 - - + -
2074C THR* 4.5 9.6 - - + +
2078C VAL* 3.5 28.5 - - + -
2089C PHE* 4.0 16.2 - - + +
2091C ARG* 3.4 38.4 - - + +
2198C GLU 3.0 19.0 + - - +
2199C SER* 3.7 4.5 - - - +
2201C THR* 1.3 79.3 - - - +
2203C LEU* 1.3 78.9 + - + +
2205C MET* 3.5 3.9 - - - +
2206C CYS* 3.1 42.8 + - - -
2213C ALA* 4.1 6.7 - - + -
2214C GLY 4.3 7.4 - - - +
2215C MET* 5.4 0.2 - - + -
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Residues in contact with LEU2203 (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 THR* 4.3 10.1 - - + +
2112C ALA* 4.3 5.8 - - - -
2113C SER* 3.6 20.9 - - - +
2130C ALA* 3.5 29.4 - - + +
2131C VAL 3.8 12.1 - - - +
2132C ALA* 4.0 15.9 - - + +
2199C SER* 2.7 26.9 + - - +
2202C LEU* 1.3 94.6 - - + +
2204C THR* 1.3 57.7 + - - +
2206C CYS* 4.0 0.2 - - - +
2207C ALA* 2.8 35.9 + - - +
2213C ALA* 4.0 16.8 - - + +
2214C GLY 4.6 11.2 - - - +
2215C MET* 5.0 2.0 - - + -
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Residues in contact with THR2204 (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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2115C ARG* 3.7 16.0 - - - +
2120C SER* 3.4 31.9 + - - +
2123C PHE* 4.6 0.9 - - + -
2124C ALA* 4.0 20.4 - - + +
2128C PHE* 4.5 5.7 - - + -
2129C PRO 4.9 0.9 - - - -
2130C ALA* 3.2 23.3 - - - +
2200C ALA 2.7 23.4 + - - -
2201C THR 4.2 0.9 - - - -
2203C LEU* 1.3 78.3 - - - +
2205C MET* 1.3 55.5 + - - +
2207C ALA* 4.1 2.9 - - - +
2208C SER* 2.7 35.5 + - - -
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Residues in contact with MET2205 (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 SER* 3.9 27.4 - - - +
2078C VAL* 3.6 43.7 - - + -
2079C GLU* 4.0 13.0 - - - +
2123C PHE* 3.6 49.6 - - + -
2201C THR* 3.1 22.4 + - - +
2202C LEU 3.5 6.3 - - - +
2204C THR* 1.3 79.0 - - - +
2206C CYS* 1.3 66.1 + - - +
2208C SER* 3.4 8.5 + - - -
2209C GLN* 2.8 39.1 + - - +
2211C LEU* 5.7 0.4 - - + -
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Residues in contact with CYS2206 (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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2078C VAL* 3.9 19.3 - - - -
2089C PHE* 3.9 14.8 - - - -
2202C LEU* 3.1 43.1 + - - +
2203C LEU 4.0 0.4 - - - +
2205C MET* 1.3 75.1 - - - +
2207C ALA* 1.3 58.2 + - - +
2208C SER 3.0 4.9 - - - -
2209C GLN* 2.9 18.0 + - - -
2210C GLY* 3.3 0.5 + - - -
2211C LEU* 3.1 45.9 + - + +
2213C ALA* 3.8 18.2 - - + -
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Residues in contact with ALA2207 (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 PHE* 3.7 23.1 - - + -
2129C PRO 4.7 0.4 - - - +
2131C VAL* 3.5 28.5 - - + +
2203C LEU 2.8 23.8 + - - +
2204C THR* 4.2 0.7 - - - +
2206C CYS* 1.3 73.5 - - - +
2208C SER* 1.3 56.8 + - - +
2209C GLN 3.4 0.4 + - - -
2210C GLY 4.7 2.5 + - - -
2211C LEU 4.3 4.0 - - - -
3155D VAL* 5.0 5.5 - - + +
3190D MET 3.5 10.4 - - - +
3191D GLY* 5.4 0.5 - - - -
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Residues in contact with SER2208 (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 PHE* 3.9 7.4 - - - +
2124C ALA* 4.4 7.2 - - - -
2128C PHE* 4.0 16.4 - - - -
2204C THR 2.7 22.0 + - - -
2205C MET* 3.4 9.9 + - - -
2207C ALA* 1.3 77.4 - - - +
2209C GLN* 1.3 59.6 + - - +
2210C GLY 3.8 1.1 - - - -
3189D ALA 4.0 1.4 - - - +
3190D MET* 3.4 34.1 - - - -
5175E ARG* 3.5 29.7 + - - -
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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