Contacts of the helix formed by residues 2203 - 2216 (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 GLY2203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2199D MET 3.1 8.7 + - - -
2200D ARG 3.3 9.4 + - - -
2201D ALA 3.2 4.3 - - - -
2202D LEU* 1.3 78.3 - - - +
2204D MET* 1.3 64.2 + - - +
2205D HIS* 3.3 4.0 - - - -
2206D GLU* 3.2 31.2 + - - +
2207D THR* 3.2 17.4 + - - +
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Residues in contact with MET2204 (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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2156D LEU* 4.8 17.7 - - + -
2160D LEU* 5.3 8.7 - - + -
2164D ARG* 6.0 0.2 - - - +
2192D PHE* 3.6 32.5 - - + -
2199D MET* 3.7 33.5 + - + +
2202D LEU* 3.5 23.8 - - + -
2203D GLY* 1.3 73.8 - - - +
2205D HIS* 1.3 63.7 + - - +
2207D THR* 2.5 31.7 + - - +
2208D VAL* 2.9 16.2 + - + +
2236D PHE* 4.4 16.8 - - + -
2240D PHE* 4.3 10.5 - - + -
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Residues in contact with HIS2205 (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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2199D MET 4.2 1.4 + - - -
2200D ARG* 3.9 34.8 - - + -
2203D GLY* 3.9 3.1 - - - -
2204D MET* 1.3 84.0 + - - +
2206D GLU* 1.3 97.5 + - - +
2208D VAL* 3.4 7.9 + - - +
2209D MET* 2.9 31.0 + - - +
2236D PHE* 5.5 2.2 - - - -
2237D LEU* 5.2 8.0 - - + +
2240D PHE* 3.7 37.3 - + + -
2250D SER* 4.4 26.2 + - - -
2251D MET* 5.1 14.5 - - - +
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Residues in contact with GLU2206 (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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2200D ARG 5.0 0.2 - - - +
2203D GLY* 3.2 18.2 - - - +
2204D MET 3.2 0.2 - - - -
2205D HIS* 1.3 120.2 + - + +
2207D THR* 1.3 56.6 + - + +
2209D MET* 3.3 7.3 + - + +
2210D GLU* 2.9 29.5 + - - +
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Residues in contact with THR2207 (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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2163D ILE* 5.1 12.1 - - - +
2164D ARG* 4.1 35.4 - - + +
2203D GLY 3.2 17.5 - - - +
2204D MET* 2.5 25.8 + - - +
2206D GLU* 1.3 77.1 - - + +
2208D VAL* 1.3 61.6 + - - +
2210D GLU* 3.3 6.4 + - - +
2211D VAL* 2.9 34.7 + - - +
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Residues in contact with VAL2208 (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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2163D ILE* 6.3 1.3 - - + -
2179D MET* 5.7 4.5 - - + -
2183D ILE* 5.3 9.6 - - + -
2186D ILE* 6.0 0.7 - - + -
2204D MET* 2.9 17.6 + - + +
2205D HIS* 4.0 4.0 - - - +
2207D THR* 1.3 86.8 + - - +
2209D MET* 1.3 58.0 + - - +
2211D VAL* 3.3 8.6 + - + +
2212D MET* 2.9 28.9 + - + +
2233D CYS* 3.9 31.9 - - + +
2236D PHE* 3.5 37.9 - - + -
2237D LEU* 4.4 16.4 - - + -
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Residues in contact with MET2209 (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 2.9 18.7 + - - +
2206D GLU* 3.6 7.9 - - - +
2208D VAL* 1.3 77.2 - - - +
2210D GLU* 1.3 56.9 + - - +
2212D MET* 3.3 30.7 + - + +
2213D VAL* 2.9 30.7 + - + +
2237D LEU* 5.3 3.3 - - + +
2251D MET* 4.0 25.1 - - + -
2254D HIS* 3.8 27.4 - - + -
2257D TYR* 4.2 19.5 - - - -
2258D LEU* 4.9 3.1 - - + -
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Residues in contact with GLU2210 (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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2206D GLU 2.9 17.4 + - - +
2207D THR* 3.3 7.4 + - - +
2209D MET* 1.3 74.3 - - - +
2211D VAL* 1.3 60.2 + - + +
2213D VAL* 3.1 13.5 - - + +
2214D ASN* 2.9 32.3 + - - +
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Residues in contact with VAL2211 (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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2163D ILE* 5.0 4.3 - - + -
2167D LEU* 3.7 30.7 - - + -
2179D MET* 3.8 23.8 - - + -
2207D THR* 2.9 22.5 + - - +
2208D VAL* 3.6 8.5 - - - +
2210D GLU* 1.3 75.0 - - + +
2212D MET* 1.3 58.2 + - - +
2214D ASN* 3.3 6.2 + - - +
2215D VAL* 2.9 31.1 + - + +
2229D MET* 3.7 31.4 - - + -
2233D CYS* 5.5 8.1 - - + -
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Residues in contact with MET2212 (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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2208D VAL* 2.9 16.3 + - + +
2209D MET* 3.6 33.0 - - + +
2210D GLU 3.2 0.2 - - - -
2211D VAL* 1.3 79.0 - - - +
2213D VAL* 1.3 57.5 + - - +
2215D VAL* 3.8 5.8 - - - -
2216D LEU* 2.9 59.5 + - + +
2230D VAL* 5.6 1.3 - - + -
2233D CYS* 4.8 20.2 - - + -
2234D CYS* 4.9 10.1 - - - -
2237D LEU* 4.4 19.3 - - + -
2257D TYR* 4.7 9.4 - - + -
2258D LEU* 3.9 25.4 - - + -
2261D ASN* 5.5 3.4 - - + +
2273D PRO* 5.1 7.6 - - - -
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Residues in contact with VAL2213 (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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2209D MET* 2.9 19.0 + - + +
2210D GLU* 3.1 22.7 - - + +
2212D MET* 1.3 76.3 - - - +
2214D ASN* 1.3 62.2 + - + +
2216D LEU* 4.2 11.6 + - - -
2257D TYR* 3.2 38.1 + - + +
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Residues in contact with ASN2214 (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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2167D LEU 4.4 15.0 + - - -
2210D GLU* 2.9 19.2 + - - +
2211D VAL* 3.7 6.1 - - - +
2213D VAL* 1.3 81.7 - - + +
2215D VAL* 1.3 60.7 + - - +
2216D LEU 4.6 2.1 - - - -
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Residues in contact with VAL2215 (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* 5.4 4.3 - - + -
2211D VAL* 2.9 24.6 + - + +
2212D MET* 3.5 11.0 - - + +
2214D ASN* 1.3 75.7 - - - +
2216D LEU* 1.3 78.9 + - + +
2225D ARG* 4.8 10.1 - - + +
2226D PHE* 3.7 37.5 - - + +
2229D MET* 4.3 22.0 - - + -
2230D VAL* 5.7 4.0 - - + +
2233D CYS* 5.6 4.5 - - - -
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Residues in contact with LEU2216 (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* 2.9 43.9 + - + +
2213D VAL* 4.2 13.0 - - - +
2214D ASN 4.6 2.7 - - - -
2215D VAL* 1.3 95.2 - - + +
2230D VAL* 4.4 20.9 - - + -
2257D TYR* 5.2 1.3 - - - +
2261D ASN* 3.5 38.4 - - + +
2273D PRO* 5.5 7.4 - - + -
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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