Contacts of the helix formed by residues 2292 - 2307 (chain B) 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 GLN2292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2290B ALA 3.4 3.3 + - - +
2291B LEU* 1.3 83.5 - - + +
2293B GLU* 1.3 63.5 + - - +
2294B GLN* 3.3 12.0 + - + +
2295B ASP* 4.2 4.2 + - + +
2296B LEU* 3.2 24.6 + - - +
3868B LYS* 3.2 34.6 - - - +
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Residues in contact with GLU2293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2292B GLN* 1.3 75.1 + - - +
2294B GLN* 1.3 59.3 + - - +
2295B ASP 3.5 0.2 - - - -
2296B LEU* 3.5 12.8 - - + +
2297B GLU* 2.9 30.0 + - - +
2353B VAL* 5.2 16.8 - - + -
2357B LEU* 4.3 10.3 - - + +
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Residues in contact with GLN2294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2292B GLN* 3.3 9.0 - - + +
2293B GLU* 1.3 74.9 - - - +
2295B ASP* 1.3 61.5 + - - +
2297B GLU* 3.3 6.4 + - - +
2298B LYS* 2.9 28.2 + - - +
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Residues in contact with ASP2295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255B LEU* 4.7 21.1 - - + +
2256B SER* 5.5 5.6 - - - -
2259B LEU* 4.5 20.5 - - + +
2291B LEU* 5.2 0.9 - - + -
2292B GLN* 4.2 8.4 + - + +
2294B GLN* 1.3 78.6 - - - +
2296B LEU* 1.3 61.3 + - + +
2298B LYS* 3.3 7.9 + - - +
2299B VAL* 2.9 31.8 + - - +
2335B PHE* 4.9 9.0 - - + -
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Residues in contact with LEU2296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2291B LEU* 3.7 30.5 - - + -
2292B GLN 3.2 24.9 - - - +
2293B GLU* 3.4 12.3 + - + +
2294B GLN 3.2 0.4 - - - -
2295B ASP* 1.3 79.1 - - + +
2297B GLU* 1.3 61.8 + - - +
2299B VAL* 3.1 5.5 - - + +
2300B VAL* 3.0 30.1 + - + +
2335B PHE* 5.0 8.3 - - + -
2336B LEU* 3.5 28.9 - - + -
2339B ALA* 5.2 5.8 - - + -
2353B VAL* 5.4 6.1 - - + -
2354B VAL* 3.8 23.1 - - + -
2357B LEU* 4.0 15.5 - - + -
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Residues in contact with GLU2297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2293B GLU 2.9 16.9 + - - +
2294B GLN* 3.7 6.7 - - - +
2296B LEU* 1.3 76.1 - - - +
2298B LYS* 1.3 53.2 + - - +
2300B VAL* 3.1 9.9 - - + +
2301B SER* 2.5 41.2 + - - +
2357B LEU* 3.7 15.4 - - + +
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Residues in contact with LYS2298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259B LEU* 5.5 7.6 - - + +
2294B GLN 2.9 17.2 + - - +
2295B ASP* 3.6 8.5 - - - +
2296B LEU 3.2 0.2 - - - -
2297B GLU* 1.3 76.4 - - - +
2299B VAL* 1.3 56.8 + - - +
2301B SER* 3.3 6.5 + - - -
2302B TYR* 2.9 52.5 + - + +
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Residues in contact with VAL2299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259B LEU* 6.1 3.8 - - + +
2295B ASP 2.9 16.7 + - - +
2296B LEU* 3.1 17.9 - - - +
2298B LYS* 1.3 75.5 - - - +
2300B VAL* 1.3 59.0 + - + +
2302B TYR* 3.3 11.9 + - + +
2303B LEU* 2.9 27.0 + - - +
2332B TYR* 4.2 21.7 - - + +
2335B PHE* 3.7 29.6 - - + -
2336B LEU* 3.8 27.8 - - + -
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Residues in contact with VAL2300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2296B LEU* 3.0 18.4 + - + +
2297B GLU* 3.1 21.5 - - + +
2299B VAL* 1.3 75.5 - - + +
2301B SER* 1.3 62.2 + - - +
2303B LEU* 3.3 7.5 + - - +
2304B ALA* 2.9 29.3 + - - +
2336B LEU* 3.9 28.9 - - + -
2354B VAL* 5.5 4.7 - - - +
2357B LEU* 4.0 35.9 - - + +
2358B LEU* 5.0 11.0 - - + -
2364B CYS* 5.0 5.4 - - + +
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Residues in contact with SER2301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2297B GLU* 2.5 25.8 + - - +
2298B LYS* 3.6 6.8 - - - -
2300B VAL* 1.3 79.6 - - - +
2302B TYR* 1.3 62.3 + - - +
2304B ALA* 3.3 6.1 + - - +
2305B GLY* 2.9 25.8 + - - -
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Residues in contact with TYR2302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259B LEU* 3.7 22.1 + - + -
2260B GLU* 4.4 13.2 + - - +
2262B SER* 5.2 0.7 - - - -
2263B GLY* 3.3 40.6 - - - +
2298B LYS* 2.9 37.3 + - + +
2299B VAL* 3.7 12.6 - - + +
2300B VAL 3.3 0.2 - - - -
2301B SER* 1.3 81.0 - - - +
2303B LEU* 1.3 58.3 + - - +
2305B GLY* 3.3 2.1 + - - +
2306B CYS* 2.9 29.6 + - - +
2332B TYR* 5.4 3.4 - - + -
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Residues in contact with LEU2303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2299B VAL 2.9 17.2 + - - +
2300B VAL* 3.7 7.6 - - - +
2301B SER 3.3 0.2 - - - -
2302B TYR* 1.3 77.0 - - - +
2304B ALA* 1.3 61.9 + - - +
2306B CYS* 3.5 11.4 + - - +
2307B GLY* 3.7 8.5 + - - -
2329B GLY* 5.8 2.8 - - - +
2332B TYR* 4.1 25.5 - - + +
2333B LEU* 5.1 15.0 - - + -
2336B LEU* 6.0 3.6 - - + -
2363B GLU 5.4 0.3 - - - +
2364B CYS* 5.0 11.5 - - + +
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Residues in contact with ALA2304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300B VAL 2.9 17.2 + - - +
2301B SER* 3.7 6.3 - - - +
2303B LEU* 1.3 79.8 - - - +
2305B GLY* 1.3 60.9 + - - +
2307B GLY 3.7 1.9 + - - -
2308B LEU* 3.4 20.8 + - - +
2361B LYS* 5.0 10.8 - - + -
2363B GLU* 4.3 16.2 - - + +
2364B CYS* 4.1 30.2 - - + +
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Residues in contact with GLY2305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2301B SER 2.9 16.0 + - - -
2302B TYR* 3.7 2.2 - - - -
2304B ALA* 1.3 74.1 - - - +
2306B CYS* 1.3 65.7 + - - +
2308B LEU* 3.6 16.9 + - - +
2309B GLN* 4.3 3.5 + - - +
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Residues in contact with CYS2306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2302B TYR 2.9 17.5 + - - +
2303B LEU* 3.7 9.9 - - - +
2304B ALA 3.2 0.6 - - - -
2305B GLY* 1.3 77.9 - - - +
2307B GLY* 1.3 58.6 + - - +
2308B LEU 3.3 0.2 - - - -
2309B GLN 3.3 17.8 - - - +
2310B SER 5.5 0.3 - - - -
2311B CYS* 5.6 1.9 - - - +
2325B ASN* 3.8 31.6 + - - +
2328B GLY* 4.1 9.4 - - - +
2329B GLY* 4.0 22.2 - - - -
2332B TYR* 5.8 1.8 - - + -
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Residues in contact with GLY2307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2303B LEU 3.7 5.9 + - - -
2304B ALA 3.7 6.3 + - - -
2305B GLY 3.5 0.2 - - - -
2306B CYS* 1.3 78.7 - - - +
2308B LEU* 1.3 62.2 + - - +
2309B GLN 3.4 1.8 - - - -
2323B GLY 4.9 0.3 - - - -
2324B TRP* 3.6 36.5 + - - +
2325B ASN 4.4 2.0 - - - -
2363B GLU 5.5 5.3 - - - +
2367B PRO* 6.0 1.0 - - - +
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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