Contacts of the helix formed by residues 2272 - 2282 (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 THR2272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2234D CYS* 4.4 5.2 - - - +
2262D SER* 5.2 7.6 - - - +
2271D SER* 1.3 77.3 + - - +
2273D PRO* 1.3 75.4 - - + +
2274D LEU* 3.6 35.4 - - + +
2275D ASP* 2.8 31.9 + - - +
2276D VAL* 3.6 3.6 + - - +
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Residues in contact with PRO2273 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2212D MET* 5.1 8.7 - - - -
2216D LEU* 5.5 7.0 - - + -
2230D VAL* 5.3 5.8 - - + -
2234D CYS* 4.0 16.4 - - - -
2237D LEU* 6.5 0.4 - - + -
2258D LEU* 3.8 34.5 - - + +
2261D ASN* 4.7 10.1 - - + +
2262D SER* 4.4 17.7 - - - +
2271D SER 4.7 0.4 - - - +
2272D THR* 1.3 91.6 - - + +
2274D LEU* 1.3 56.3 + - - +
2276D VAL* 3.2 15.6 + - + +
2277D ALA* 2.9 26.7 + - - +
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Residues in contact with LEU2274 (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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2262D SER* 3.9 26.4 - - - +
2263D GLY 5.6 2.5 - - - +
2272D THR* 3.0 27.8 + - + +
2273D PRO* 1.3 79.3 - - - +
2275D ASP* 1.3 66.1 + - + +
2277D ALA* 3.3 9.3 + - - +
2278D ALA* 2.9 30.1 + - + +
2331D ARG* 3.5 42.4 - - + +
2332D TYR* 5.7 1.6 - - - -
2334D ASP* 6.0 1.8 - - + -
2335D PHE* 4.4 11.7 - - + +
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Residues in contact with ASP2275 (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* 4.4 13.3 - - - -
2271D SER* 5.8 1.3 - - - -
2272D THR* 2.8 19.6 + - - +
2274D LEU* 1.3 85.8 - - + +
2276D VAL* 1.3 59.0 + - - +
2278D ALA* 3.3 6.8 + - - +
2279D ALA* 2.9 29.8 + - - +
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Residues in contact with VAL2276 (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* 3.9 20.0 - - + +
2237D LEU* 4.0 15.3 - - + -
2238D CYS* 3.7 23.6 - - - -
2241D CYS* 4.1 16.5 - - - -
2251D MET* 3.9 19.5 - - + -
2258D LEU* 3.8 19.3 - - + -
2272D THR 4.3 2.5 - - - +
2273D PRO* 3.2 20.1 + - + +
2275D ASP* 1.3 76.5 - - - +
2277D ALA* 1.3 59.5 + - - +
2279D ALA* 3.3 3.7 + - - +
2280D SER* 2.9 27.8 + - - +
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Residues in contact with ALA2277 (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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2255D LEU* 3.9 14.1 - - + -
2258D LEU* 4.4 13.4 - - + +
2259D LEU* 5.4 5.6 - - + +
2273D PRO 2.9 12.7 + - - +
2274D LEU* 3.5 11.7 - - - +
2275D ASP 3.3 0.2 - - - -
2276D VAL* 1.3 78.9 - - - +
2278D ALA* 1.3 56.8 + - - +
2280D SER* 2.5 22.9 + - - -
2281D VAL* 2.9 20.4 + - - +
2335D PHE* 3.7 21.3 - - + -
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Residues in contact with ALA2278 (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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2274D LEU* 2.9 17.2 + - + +
2275D ASP* 3.3 7.2 + - - +
2277D ALA* 1.3 76.7 - - - +
2279D ALA* 1.3 58.1 + - - +
2281D VAL* 3.5 3.9 + - - +
2282D ILE* 3.0 31.3 + - - +
2334D ASP* 5.2 0.7 - - + -
2335D PHE* 4.0 22.1 - - + +
2338D PHE* 3.6 34.9 - - + +
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Residues in contact with ALA2279 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2238D CYS* 4.9 11.0 - - + +
2241D CYS* 4.9 13.7 - - + +
2242D ARG* 5.3 13.7 - - + +
2248D GLN* 3.4 11.6 + - - -
2275D ASP 2.9 18.5 + - - +
2276D VAL* 3.7 7.4 - - - +
2277D ALA 3.2 0.2 - - - -
2278D ALA* 1.3 76.0 - - - +
2280D SER* 1.3 61.4 + - - +
2282D ILE* 3.3 24.2 - - + +
2283D ASP* 5.5 0.2 - - - +
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Residues in contact with SER2280 (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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2241D CYS* 5.1 3.3 - - - +
2248D GLN* 2.9 39.0 + - - +
2251D MET* 5.1 12.8 - - - -
2252D PHE* 5.0 14.6 - - - -
2255D LEU* 4.1 10.2 - - - +
2258D LEU* 5.2 2.8 - - - +
2276D VAL* 2.9 14.3 + - - -
2277D ALA* 2.5 27.5 + - - -
2279D ALA* 1.3 77.1 - - - +
2281D VAL* 1.3 59.6 + - - +
2282D ILE 3.7 1.7 + - - +
2287D LEU* 3.6 12.6 - - - +
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Residues in contact with VAL2281 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2252D PHE* 5.6 1.3 - - + -
2255D LEU* 4.2 16.6 - - + -
2277D ALA 2.9 17.3 + - - +
2278D ALA* 4.1 4.0 - - - +
2280D SER* 1.3 78.3 - - - +
2282D ILE* 1.3 64.3 + - - +
2283D ASP 3.9 0.2 + - - -
2284D ASN 4.0 9.7 + - - +
2287D LEU* 3.8 25.1 - - + +
2288D ALA* 5.2 6.4 - - + +
2291D LEU* 4.3 16.6 - - + -
2335D PHE* 4.1 22.0 - - + +
2338D PHE 4.9 2.7 - - - +
2339D ALA* 4.0 33.0 - - + +
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Residues in contact with ILE2282 (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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2248D GLN* 4.3 4.0 + - - -
2278D ALA 3.0 17.1 + - - +
2279D ALA* 3.3 27.4 - - + +
2280D SER 3.8 4.7 - - - +
2281D VAL* 1.3 79.3 - - - +
2283D ASP* 1.3 84.9 + - + +
2284D ASN* 3.4 1.6 + - - +
2337D ARG* 6.2 0.2 - - - +
2338D PHE* 3.2 41.9 + - + +
2341D PHE* 3.7 17.9 - - + +
2342D VAL* 5.6 0.9 - - - -
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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