Contacts of the helix formed by residues 2025 - 2032 (chain C) in PDB entry 2QRA
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 GLU2025 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2022C GLU* 3.4 26.7 + - - +
2023C PHE 2.9 7.3 - - - +
2024C VAL* 1.3 87.6 - - + +
2026C GLU* 1.3 66.5 + - - +
2027C PHE* 4.4 8.3 + - + +
2028C ASN* 3.1 29.1 + - - +
2029C ARG* 3.2 8.5 + - - -
2099C GLU* 4.9 9.0 - - - +
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Residues in contact with GLU2026 (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 3.8 3.4 + - - -
2025C GLU* 1.3 73.7 + - - +
2027C PHE* 1.3 58.2 + - - +
2029C ARG* 3.1 28.8 + - - +
2030C LEU* 2.9 32.7 + - + +
2045C SER* 4.5 1.7 - - - +
2048C ALA* 4.2 6.2 - - + +
2049C ARG* 3.0 66.1 + - - +
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Residues in contact with PHE2027 (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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2025C GLU* 3.2 7.2 + - + +
2026C GLU* 1.3 79.4 - - - +
2028C ASN* 1.3 72.8 + - - +
2030C LEU* 3.3 16.0 + - + +
2031C LYS* 3.1 56.4 + - + +
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Residues in contact with ASN2028 (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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2021C GLU* 3.6 26.1 - - - +
2022C GLU* 2.7 44.9 + - - +
2023C PHE* 3.4 17.4 - - + -
2025C GLU* 3.1 16.1 + - - +
2027C PHE* 1.3 87.2 - - - +
2029C ARG* 1.3 65.1 + - - +
2031C LYS* 3.3 26.8 + - - +
2032C THR* 3.7 1.9 - - - +
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Residues in contact with ARG2029 (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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2023C PHE* 2.9 39.5 + - + +
2024C VAL 3.2 19.0 + - - -
2025C GLU 3.2 2.3 + - - +
2026C GLU* 3.1 32.1 + - - +
2028C ASN* 1.3 76.7 - - - +
2030C LEU* 1.3 62.4 + - - +
2032C THR* 2.8 25.1 + - - -
2033C PHE* 3.3 9.2 - - - -
2048C ALA* 2.7 32.5 + - + -
2049C ARG* 4.0 4.4 + - - +
2051C GLY* 3.3 33.8 - - - -
2052C PHE 3.6 11.7 - - - +
2053C LEU* 3.5 21.1 - - + -
2064C PHE* 3.6 15.7 - - - -
2092C PHE* 3.8 20.6 - - - -
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Residues in contact with LEU2030 (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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2026C GLU* 2.9 22.0 + - + +
2027C PHE* 3.5 16.4 - - + +
2028C ASN 3.2 0.2 - - - -
2029C ARG* 1.3 75.6 - - - +
2031C LYS* 1.3 64.4 + - - +
2033C PHE* 3.1 17.7 + - + +
2034C ALA 4.6 0.2 + - - -
2044C ALA* 3.9 39.7 - - + +
2045C SER* 4.0 14.8 - - - +
2048C ALA* 3.9 10.3 - - + +
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Residues in contact with LYS2031 (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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2021C GLU* 4.9 10.8 + - - +
2027C PHE* 3.1 51.5 + - + +
2028C ASN* 3.5 19.9 + - - +
2029C ARG 3.2 0.6 - - - -
2030C LEU* 1.3 76.6 - - - +
2032C THR* 1.3 60.3 + - + +
2033C PHE 3.1 4.4 + - - -
2034C ALA* 3.6 15.4 + - - +
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Residues in contact with THR2032 (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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2021C GLU* 4.9 1.3 - - - +
2023C PHE* 3.7 36.1 - - + -
2028C ASN 3.7 2.2 - - - +
2029C ARG 2.8 17.6 + - - +
2030C LEU 3.1 2.0 - - - -
2031C LYS* 1.3 78.5 - - + +
2033C PHE* 1.3 55.1 + - - +
2034C ALA* 3.3 5.1 + - - +
2035C ASN 5.0 0.2 + - - -
2053C LEU* 3.6 9.0 - - + -
2054C TYR* 2.9 50.3 + - - +
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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