Contacts of the helix formed by residues 2207 - 2228 (chain A) in PDB entry 4UXL
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 THR2207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2071A GLU* 5.0 8.5 - - - +
2144A VAL* 5.0 1.3 - - - -
2205A ARG 5.1 2.2 - - - +
2206A PRO* 1.3 75.8 - - + +
2208A PHE* 1.3 59.7 + - - +
2209A HIS* 3.5 9.0 + - - +
2210A ARG* 3.2 23.8 + - + +
2211A ILE* 2.9 31.9 + - - +
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Residues in contact with PHE2208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2064A SER* 4.7 5.1 - - - +
2067A CYS* 3.3 49.6 - - + -
2068A VAL* 3.8 18.2 - - - +
2071A GLU* 3.8 21.8 + - + +
2140A THR* 3.7 32.1 - - - -
2143A ASP* 4.0 15.7 - - + -
2144A VAL* 3.9 27.3 - - + +
2147A PHE* 4.1 20.2 - + + -
2207A THR* 1.3 71.0 - - - +
2209A HIS* 1.3 61.3 + - - +
2211A ILE* 3.3 15.1 + - + +
2212A GLN* 2.9 29.6 + - - +
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Residues in contact with HIS2209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2068A VAL* 3.8 31.6 - - + +
2071A GLU* 4.4 11.3 + - - -
2072A ARG* 4.4 15.0 + - + -
2207A THR* 3.3 8.8 + - - +
2208A PHE* 1.3 76.3 - - - +
2210A ARG* 1.3 58.8 + - - +
2212A GLN* 3.2 8.5 + - - +
2213A ASP* 2.8 41.8 + - - +
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Residues in contact with ARG2210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2206A PRO* 4.3 18.8 - - + +
2207A THR* 3.2 21.6 + - + +
2209A HIS* 1.3 78.3 - - - +
2211A ILE* 1.3 54.3 + - - +
2213A ASP* 3.2 11.9 + - + +
2214A GLN* 2.7 60.3 + - + +
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Residues in contact with ILE2211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2064A SER* 4.4 4.0 - - - -
2144A VAL* 3.9 17.3 - - + -
2147A PHE* 3.4 33.4 - - + -
2193A LEU* 4.0 24.0 - - + -
2197A CYS* 3.8 24.0 - - - -
2206A PRO* 3.9 16.6 - - + -
2207A THR 2.9 23.4 + - - +
2208A PHE* 3.5 21.5 - - + +
2210A ARG* 1.3 77.6 - - - +
2212A GLN* 1.3 61.1 + - - +
2214A GLN* 3.5 1.7 + - - +
2215A LEU* 3.1 26.2 + - + +
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Residues in contact with GLN2212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2061A VAL* 4.8 2.0 - - + +
2064A SER* 3.4 24.4 + - - +
2065A LYS* 3.8 25.5 - - + +
2068A VAL* 3.3 28.8 - - + +
2208A PHE 2.9 15.8 + - - +
2209A HIS* 3.6 9.4 - - - +
2211A ILE* 1.3 74.7 - - - +
2213A ASP* 1.3 68.9 + - - +
2215A LEU* 3.3 3.3 + - + +
2216A GLN* 2.8 56.0 + - - +
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Residues in contact with ASP2213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209A HIS* 2.8 30.2 + - - +
2210A ARG* 3.3 12.8 - - + +
2212A GLN* 1.3 78.1 - - - +
2214A GLN* 1.3 54.4 + - + +
2216A GLN* 3.1 12.8 + - - +
2217A LEU* 2.7 49.8 + - + +
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Residues in contact with GLN2214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189A ASP* 5.1 10.7 + - - +
2190A LEU* 6.2 0.4 - - - -
2192A ASN* 6.4 0.6 - - - +
2193A LEU* 4.3 27.5 - - + +
2210A ARG* 2.7 52.5 + - + +
2211A ILE 3.8 4.7 - - - +
2213A ASP* 1.3 73.2 - - + +
2215A LEU* 1.3 58.7 + - - +
2217A LEU* 3.7 16.4 - - - +
2218A PHE* 2.9 31.7 + - - +
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Residues in contact with LEU2215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2057A VAL* 4.3 8.7 - - + +
2060A CYS* 3.4 50.0 - - + +
2061A VAL* 3.8 16.4 - - + +
2064A SER* 3.8 15.7 - - - +
2147A PHE* 4.3 8.1 - - + -
2151A ILE* 5.4 2.5 - - + -
2190A LEU* 3.9 20.4 - - + -
2193A LEU* 3.7 22.0 - - + -
2211A ILE* 3.1 24.2 + - + +
2212A GLN* 3.6 4.7 - - - +
2214A GLN* 1.3 77.4 - - - +
2216A GLN* 1.3 61.9 + - - +
2218A PHE* 3.4 4.3 + - - +
2219A ARG* 3.1 22.7 + - - +
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Residues in contact with GLN2216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2061A VAL* 3.8 9.3 - - + +
2065A LYS* 3.6 17.8 - - - -
2212A GLN* 2.8 52.1 + - - +
2213A ASP* 3.8 10.0 + - - +
2215A LEU* 1.3 73.6 - - - +
2217A LEU* 1.3 67.0 + - + +
2219A ARG* 3.2 26.6 + - - +
2220A ASN* 3.1 23.7 + - - +
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Residues in contact with LEU2217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2213A ASP* 2.7 34.7 + - + +
2214A GLN* 3.7 18.6 - - - +
2216A GLN* 1.3 74.3 - - + +
2218A PHE* 1.3 62.2 + - - +
2220A ASN* 3.5 6.9 + - + +
2221A PHE* 3.0 23.0 + - - +
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Residues in contact with PHE2218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2053A LEU* 4.6 3.8 - - + -
2057A VAL* 3.9 27.8 - - + -
2187A PRO* 3.5 34.5 - - + -
2189A ASP* 3.2 38.1 - - + +
2190A LEU* 3.8 28.0 - - + -
2214A GLN 2.9 18.9 + - - +
2215A LEU 3.8 3.1 - - - +
2216A GLN 3.3 0.2 - - - -
2217A LEU* 1.3 77.1 - - - +
2219A ARG* 1.3 64.5 + - - +
2221A PHE* 3.3 22.2 + + - +
2222A PHE* 2.9 43.8 + + + +
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Residues in contact with ARG2219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2054A VAL* 5.2 7.4 - - + -
2057A VAL* 3.8 21.1 - - + -
2058A ASP* 3.6 20.8 + - - +
2061A VAL* 4.2 20.0 - - - +
2065A LYS* 5.5 3.6 - - - +
2215A LEU 3.1 17.4 + - - +
2216A GLN* 3.2 28.8 + - - +
2218A PHE* 1.3 82.1 - - - +
2220A ASN* 1.3 58.1 + - - +
2222A PHE* 3.2 6.6 + - + +
2223A LEU* 2.9 62.1 + - + +
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Residues in contact with ASN2220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2216A GLN 3.1 13.7 + - - +
2217A LEU* 3.9 7.6 + - + +
2219A ARG* 1.3 77.1 - - - +
2221A PHE* 1.3 68.6 + - - +
2223A LEU* 4.4 9.8 - - - +
2224A ASN* 2.9 56.5 + - - +
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Residues in contact with PHE2221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189A ASP* 4.1 13.7 - - - -
2217A LEU 3.0 18.0 + - - +
2218A PHE* 3.6 28.0 - + - +
2220A ASN* 1.3 79.9 - - - +
2222A PHE* 1.3 66.8 + + + +
2224A ASN* 3.6 6.5 + - - +
2225A SER* 2.9 41.1 + - - -
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Residues in contact with PHE2222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2053A LEU* 4.1 32.8 - - + -
2054A VAL* 4.7 22.0 - - + -
2057A VAL* 6.4 0.9 - - + -
2218A PHE* 2.9 36.6 + + + +
2219A ARG* 3.7 5.8 - - + +
2220A ASN 3.1 0.2 - - - -
2221A PHE* 1.3 84.9 - + + +
2223A LEU* 1.3 75.3 + - + +
2225A SER* 3.2 23.2 - - - -
2226A ILE* 3.2 19.3 + - + +
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Residues in contact with LEU2223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2054A VAL* 4.5 22.7 - - + -
2219A ARG* 2.9 47.0 + - + +
2220A ASN* 3.7 9.0 - - - +
2222A PHE* 1.3 80.7 - - + +
2224A ASN* 1.3 67.0 + - - +
2226A ILE* 2.8 27.2 - - + +
2227A TYR* 3.1 36.0 - - + +
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Residues in contact with ASN2224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2220A ASN* 2.9 52.3 + - - +
2221A PHE* 3.6 5.6 + - - +
2223A LEU* 1.3 74.3 - - - +
2225A SER* 1.3 63.0 + - - +
2226A ILE 3.3 0.5 + - - -
2227A TYR* 3.4 10.5 + - - +
2228A LYS* 3.3 24.9 + - - +
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Residues in contact with SER2225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2221A PHE* 2.9 32.3 + - - -
2222A PHE* 3.2 22.2 - - - -
2223A LEU 3.1 0.4 - - - -
2224A ASN* 1.3 77.6 - - - +
2226A ILE* 1.3 62.1 - - - +
2228A LYS* 3.3 26.6 - - - +
2229A SER* 3.2 10.9 + - - -
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Residues in contact with ILE2226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2222A PHE* 3.2 17.2 + - + +
2223A LEU* 2.8 32.1 - - + +
2225A SER* 1.3 78.2 - - - +
2227A TYR* 1.3 90.9 + - + +
2229A SER* 2.8 29.2 + - - +
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Residues in contact with TYR2227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2223A LEU* 3.1 47.2 - - + +
2224A ASN* 3.4 12.5 + - - +
2225A SER 3.4 0.4 - - - -
2226A ILE* 1.3 100.3 - - + +
2228A LYS* 1.3 61.5 + - - +
2229A SER 3.0 5.9 + - - -
2230A ARG 3.9 5.7 + - - -
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Residues in contact with LYS2228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2224A ASN 3.3 11.7 + - - +
2225A SER* 3.3 29.6 - - - +
2227A TYR* 1.3 77.3 - - - +
2229A SER* 1.3 82.6 + - - +
2230A ARG 3.2 1.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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