Contacts of the helix formed by residues 2226 - 2242 (chain D) in PDB entry 6X34
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 PHE2226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2171D MET* 3.7 37.7 - - + -
2172D GLY* 4.5 15.5 - - - -
2173D PRO* 5.2 4.9 - - + -
2176D GLU* 5.0 8.3 - - + -
2215D VAL* 3.7 24.6 - - + +
2225D ARG* 1.3 84.8 - - + +
2227D PRO* 1.3 73.4 - - - +
2228D LYS 3.4 2.2 - - - -
2229D MET* 3.8 24.7 - - + +
2230D VAL* 3.2 18.9 + - - +
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Residues in contact with PRO2227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2225D ARG* 4.6 3.6 - - - +
2226D PHE* 1.3 86.4 - - - +
2228D LYS* 1.3 67.1 + - - +
2230D VAL* 3.1 12.6 - - + +
2231D THR* 2.9 31.8 + - + +
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Residues in contact with LYS2228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2180D ILE* 3.6 23.7 - - + +
2226D PHE 3.4 0.2 - - - -
2227D PRO* 1.3 81.4 - - - +
2229D MET* 1.3 57.8 + - - +
2231D THR* 2.7 21.6 + - - -
2232D SER* 2.8 19.8 + - - -
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Residues in contact with MET2229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2171D MET* 4.8 12.8 - - + -
2176D GLU* 4.5 23.5 - - + +
2179D MET* 3.6 33.2 - - + -
2180D ILE* 4.4 6.8 - - + +
2211D VAL* 3.7 27.1 - - + -
2215D VAL* 4.3 25.6 - - + -
2226D PHE* 3.4 28.8 + - + +
2227D PRO 3.2 0.8 - - - -
2228D LYS* 1.3 78.8 - - - +
2230D VAL* 1.3 58.7 + - - +
2232D SER* 2.5 21.5 + - - +
2233D CYS* 3.0 21.0 + - + +
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Residues in contact with VAL2230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212D MET* 5.6 1.8 - - + -
2215D VAL* 5.7 3.8 - - + -
2216D LEU* 4.4 23.6 - - + -
2225D ARG 5.0 3.8 - - - +
2226D PHE 3.2 11.7 + - - +
2227D PRO* 3.1 21.8 - - + +
2229D MET* 1.3 77.2 - - - +
2231D THR* 1.3 69.5 + - + +
2233D CYS* 3.1 11.4 - - - -
2234D CYS* 2.9 46.6 + - - -
2271D SER 5.1 6.3 - - - +
2273D PRO* 5.3 5.4 - - + -
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Residues in contact with THR2231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2227D PRO* 2.9 22.9 + - + +
2228D LYS* 2.7 26.2 + - - -
2230D VAL* 1.3 81.8 - - + +
2232D SER* 1.3 56.4 + - - +
2235D ARG* 2.9 39.9 + - - +
2271D SER* 3.7 31.0 - - - +
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Residues in contact with SER2232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2179D MET* 5.8 1.7 - - - +
2180D ILE* 4.0 20.3 - - - +
2183D ILE* 3.8 25.2 - - - +
2228D LYS 2.8 15.4 + - - -
2229D MET* 2.5 26.9 + - - +
2231D THR* 1.3 76.7 + - - +
2233D CYS* 1.3 55.7 + - - -
2235D ARG* 3.3 15.4 + - - +
2236D PHE* 2.9 27.7 + - - +
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Residues in contact with CYS2233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2179D MET* 5.9 3.8 - - + -
2183D ILE* 5.2 5.1 - - + +
2208D VAL* 3.9 22.9 - - + +
2211D VAL* 5.5 7.9 - - + -
2212D MET* 4.8 20.9 - - + -
2215D VAL* 5.6 3.4 - - - -
2229D MET* 3.0 22.0 + - + +
2230D VAL* 3.1 34.3 - - - -
2232D SER* 1.3 77.3 + - - +
2234D CYS* 1.3 60.2 + - - +
2236D PHE* 3.3 7.3 + - - +
2237D LEU* 2.9 33.9 + - + +
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Residues in contact with CYS2234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212D MET* 4.9 9.6 - - - -
2230D VAL* 2.9 43.2 + - - +
2233D CYS* 1.3 78.6 - - - +
2235D ARG* 1.3 59.9 + - - +
2237D LEU* 3.3 9.0 + - - +
2238D CYS* 2.9 34.1 + - - +
2271D SER* 3.7 23.3 - - - -
2272D THR 4.4 2.9 - - - +
2273D PRO* 4.0 25.6 - - - -
2276D VAL* 3.9 10.3 - - + +
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Residues in contact with ARG2235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2183D ILE* 5.8 1.8 - - - +
2187D MET* 4.1 30.9 - - - +
2231D THR* 2.9 27.0 + - - +
2232D SER* 3.6 11.8 + - - +
2234D CYS* 1.3 78.2 - - - +
2236D PHE* 1.3 57.1 + - - +
2238D CYS* 3.3 6.3 + - - +
2239D TYR* 2.9 51.8 + - + -
2271D SER* 4.5 10.5 - - - -
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Residues in contact with PHE2236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2183D ILE* 3.8 17.0 - - + -
2186D ILE* 3.5 35.0 - - + -
2187D MET* 4.0 23.4 - - + -
2192D PHE* 4.3 22.4 - + - -
2204D MET* 4.4 30.5 - - + -
2205D HIS* 5.4 1.6 - - - -
2208D VAL* 3.5 36.6 - - + -
2232D SER 2.9 15.8 + - - +
2233D CYS* 3.3 5.4 + - - +
2235D ARG* 1.3 76.1 - - - +
2237D LEU* 1.3 63.4 + - + +
2239D TYR* 3.3 6.9 + - + +
2240D PHE* 2.9 35.4 + + + +
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Residues in contact with LEU2237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2205D HIS* 5.2 12.3 - - + +
2208D VAL* 4.4 25.4 - - + +
2209D MET* 5.3 2.7 - - + +
2212D MET* 4.4 28.7 - - + -
2233D CYS 2.9 20.5 + - - +
2234D CYS* 3.6 9.2 - - + +
2235D ARG 3.3 0.2 - - - -
2236D PHE* 1.3 79.6 - - + +
2238D CYS* 1.3 57.7 + - - +
2240D PHE* 2.9 9.7 + - + +
2241D CYS* 2.9 35.6 + - - -
2251D MET* 3.7 33.7 - - + -
2258D LEU* 5.3 1.6 - - + -
2273D PRO* 6.5 0.2 - - + -
2276D VAL* 4.0 20.2 - - + -
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Residues in contact with CYS2238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2234D CYS* 2.9 20.3 + - - +
2235D ARG* 3.7 7.2 - - - +
2237D LEU* 1.3 76.3 - - - +
2239D TYR* 1.3 65.7 + - + +
2240D PHE 3.4 0.2 + - - -
2241D CYS* 3.6 13.4 + - - +
2242D ARG* 3.6 25.0 + - - +
2275D ASP* 4.4 12.1 - - - -
2276D VAL* 3.7 30.3 - - - +
2279D ALA* 4.9 8.8 - - + +
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Residues in contact with TYR2239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2187D MET* 3.7 34.5 - - + -
2192D PHE* 5.2 6.3 - - + -
2193D TYR* 3.9 24.5 - + - -
2235D ARG* 2.9 45.3 + - + +
2236D PHE* 3.7 8.7 - - + +
2238D CYS* 1.3 78.0 - - + +
2240D PHE* 1.3 61.4 + - - +
2242D ARG* 3.8 30.8 + - - +
2243D ILE* 3.3 22.6 + - - +
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Residues in contact with PHE2240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2192D PHE* 3.5 33.0 - + + -
2199D MET* 4.2 15.5 - - + -
2200D ARG* 4.9 2.0 - - + -
2204D MET* 4.3 8.5 - - + -
2205D HIS* 3.7 43.1 - + + -
2236D PHE* 2.9 29.4 + + + +
2237D LEU* 2.9 12.5 + - + +
2239D TYR* 1.3 76.8 - - - +
2241D CYS* 1.3 67.4 + - - +
2243D ILE* 3.3 15.9 + - - +
2247D ASN* 3.3 56.7 + - + +
2250D SER* 5.6 1.6 - - - -
2251D MET* 5.3 10.5 - - + -
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Residues in contact with CYS2241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2237D LEU* 2.9 30.6 + - - +
2238D CYS* 3.6 6.0 + - - +
2239D TYR 3.5 0.4 - - - -
2240D PHE* 1.3 80.1 - - - +
2242D ARG* 1.3 58.3 + - + +
2243D ILE 3.2 4.5 + - - -
2244D SER 3.8 13.3 - - - +
2247D ASN* 4.9 6.5 - - - -
2248D GLN* 4.0 28.5 + - - +
2251D MET* 3.7 30.5 - - + -
2276D VAL* 4.1 20.0 - - - -
2279D ALA* 4.9 12.6 - - + +
2280D SER* 5.2 2.0 - - - -
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Residues in contact with ARG2242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238D CYS* 3.6 20.3 + - - +
2239D TYR* 3.8 38.7 + - - +
2240D PHE 3.3 1.0 - - - -
2241D CYS* 1.3 79.7 - - + +
2243D ILE* 1.3 66.9 + - - +
2244D SER 3.8 0.2 - - - -
2279D ALA* 5.3 11.0 - - + +
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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