Contacts of the helix formed by residues 2292 - 2307 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2252H PHE* 5.9 0.2 - - - -
2290H ALA 3.4 3.9 + - - +
2291H LEU* 1.3 81.7 - - + +
2293H GLU* 1.3 62.6 + - - +
2294H GLN* 3.3 12.2 + - + +
2295H ASP* 4.2 4.0 + - + +
2296H LEU* 3.2 24.7 + - - +
3868H LYS* 3.2 34.1 - - - +
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Residues in contact with GLU2293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2291H LEU 4.1 0.6 + - - -
2292H GLN* 1.3 75.7 + - - +
2294H GLN* 1.3 58.5 + - - +
2295H ASP 3.5 0.4 - - - -
2296H LEU* 3.5 12.8 - - + +
2297H GLU* 2.9 29.6 + - - +
2353H VAL* 5.2 16.6 - - + -
2357H LEU* 4.3 10.5 - - + +
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Residues in contact with GLN2294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2292H GLN* 3.3 9.2 - - + +
2293H GLU* 1.3 74.9 - - - +
2295H ASP* 1.3 62.5 + - - +
2297H GLU* 3.3 7.3 + - - +
2298H LYS* 2.9 28.2 + - - +
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Residues in contact with ASP2295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255H LEU* 4.7 21.3 - - + +
2256H SER* 5.5 5.6 - - - -
2259H LEU* 4.5 20.1 - - + +
2291H LEU* 5.2 1.3 - - + -
2292H GLN* 4.2 8.0 + - + +
2293H GLU 3.5 0.2 - - - -
2294H GLN* 1.3 79.5 - - - +
2296H LEU* 1.3 61.8 + - + +
2298H LYS* 3.3 7.2 + - - +
2299H VAL* 2.9 31.5 + - - +
2335H PHE* 4.9 8.5 - - + -
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Residues in contact with LEU2296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2291H LEU* 3.7 30.3 - - + -
2292H GLN 3.2 24.9 - - - +
2293H GLU* 3.4 13.0 + - - +
2294H GLN 3.2 0.4 - - - -
2295H ASP* 1.3 78.6 - - + +
2297H GLU* 1.3 63.3 + - - +
2299H VAL* 3.1 5.3 - - + +
2300H VAL* 3.0 30.7 + - + +
2335H PHE* 5.0 8.1 - - + -
2336H LEU* 3.5 28.9 - - + -
2339H ALA* 5.2 6.1 - - + -
2353H VAL* 5.4 7.0 - - + -
2354H VAL* 3.8 22.9 - - + -
2357H LEU* 4.0 14.8 - - + -
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Residues in contact with GLU2297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2293H GLU 2.9 18.2 + - - +
2294H GLN* 3.7 5.6 - - - +
2296H LEU* 1.3 74.6 - - - +
2298H LYS* 1.3 54.4 + - - +
2300H VAL* 3.1 11.4 - - + +
2301H SER* 2.5 40.4 + - - +
2357H LEU* 3.7 15.6 - - + +
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Residues in contact with LYS2298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259H LEU* 5.5 6.7 - - + -
2294H GLN 2.9 17.2 + - - +
2295H ASP* 3.6 8.5 - - - +
2296H LEU 3.2 0.2 - - - -
2297H GLU* 1.3 77.5 - - - +
2299H VAL* 1.3 57.6 + - - +
2301H SER* 3.3 7.1 + - - -
2302H TYR* 2.9 52.1 + - + +
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Residues in contact with VAL2299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259H LEU* 6.1 3.8 - - + +
2295H ASP 2.9 15.8 + - - +
2296H LEU* 3.1 18.2 - - - +
2298H LYS* 1.3 78.0 - - - +
2300H VAL* 1.3 57.4 + - + +
2302H TYR* 3.3 12.2 + - + +
2303H LEU* 2.9 27.5 + - - +
2332H TYR* 4.2 22.1 - - + +
2335H PHE* 3.7 29.2 - - + -
2336H LEU* 3.8 28.5 - - + -
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Residues in contact with VAL2300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2296H LEU* 3.0 17.9 + - + +
2297H GLU* 3.1 22.4 - - + +
2299H VAL* 1.3 74.8 - - + +
2301H SER* 1.3 62.7 + - - +
2303H LEU* 3.3 6.7 + - - +
2304H ALA* 2.9 28.9 + - - +
2336H LEU* 3.9 29.2 - - + -
2354H VAL* 5.5 4.5 - - + +
2357H LEU* 4.0 34.5 - - + +
2358H LEU* 5.0 11.9 - - + +
2364H CYS* 5.0 5.4 - - + +
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Residues in contact with SER2301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2297H GLU* 2.5 26.6 + - - +
2298H LYS* 3.6 6.8 - - - -
2300H VAL* 1.3 79.5 - - - +
2302H TYR* 1.3 62.2 + - - +
2304H ALA* 3.3 6.7 + - - +
2305H GLY* 2.9 25.6 + - - -
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Residues in contact with TYR2302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259H LEU* 3.7 22.2 + - + -
2260H GLU* 4.4 13.3 + - - +
2262H SER* 5.2 0.7 - - - -
2263H GLY* 3.3 42.0 - - - +
2298H LYS* 2.9 38.8 + - + +
2299H VAL* 3.7 11.9 - - + +
2301H SER* 1.3 82.2 - - - +
2303H LEU* 1.3 56.1 + - - +
2305H GLY* 3.3 1.5 + - - -
2306H CYS* 2.9 30.1 + - - +
2332H TYR* 5.4 3.8 - - + -
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Residues in contact with LEU2303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2299H VAL* 2.9 18.0 + - + +
2300H VAL* 3.7 7.4 - - - +
2302H TYR* 1.3 76.1 - - - +
2304H ALA* 1.3 62.5 + - - +
2306H CYS* 3.5 11.6 + - - +
2307H GLY* 3.7 8.1 + - - -
2329H GLY* 5.8 2.8 - - - +
2332H TYR* 4.1 25.0 - - + +
2333H LEU* 5.1 14.1 - - + -
2336H LEU* 6.0 3.4 - - + -
2363H GLU 5.4 0.2 - - - +
2364H CYS* 5.0 10.9 - - + +
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Residues in contact with ALA2304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300H VAL 2.9 18.1 + - - +
2301H SER* 3.7 6.5 - - - +
2303H LEU* 1.3 79.1 - - - +
2305H GLY* 1.3 60.3 + - - +
2307H GLY* 3.7 1.6 + - - -
2308H LEU* 3.4 21.0 + - - +
2361H LYS* 5.0 10.3 - - + -
2363H GLU* 4.3 15.1 - - + +
2364H CYS* 4.1 30.2 - - + +
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Residues in contact with GLY2305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2301H SER 2.9 16.0 + - - -
2302H TYR* 3.7 1.8 - - - -
2304H ALA* 1.3 74.1 - - - +
2306H CYS* 1.3 66.3 + - - +
2308H LEU* 3.6 17.0 + - - +
2309H GLN* 4.3 3.1 + - - +
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Residues in contact with CYS2306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2302H TYR 2.9 18.1 + - - +
2303H LEU* 3.7 9.4 - - - +
2304H ALA 3.2 0.4 - - - -
2305H GLY* 1.3 79.4 - - - +
2307H GLY* 1.3 57.6 + - - +
2309H GLN 3.3 18.2 - - - +
2310H SER 5.5 0.3 - - - -
2311H CYS* 5.6 1.9 - - - +
2325H ASN* 3.8 31.6 + - - +
2328H GLY* 4.1 8.7 - - - +
2329H GLY* 4.0 23.1 - - - -
2332H TYR* 5.8 1.8 - - + -
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Residues in contact with GLY2307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2303H LEU 3.7 6.1 + - - -
2304H ALA 3.7 6.1 + - - -
2306H CYS* 1.3 78.6 - - - +
2308H LEU* 1.3 63.8 + - - +
2309H GLN 3.4 1.8 - - - -
2323H GLY 4.9 0.2 - - - -
2324H TRP* 3.6 36.6 + - - +
2325H ASN 4.4 1.6 - - - -
2363H GLU 5.5 5.3 - - - +
2367H PRO* 6.0 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
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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