Contacts of the helix formed by residues 2325 - 2341 (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 ASN2325 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2306H CYS* 3.8 29.9 + - - +
2307H GLY* 4.4 1.3 - - - -
2309H GLN 4.8 0.2 + - - -
2311H CYS* 4.2 13.2 - - + +
2314H LEU* 3.7 30.1 - - + -
2322H ILE* 5.3 0.2 - - - -
2323H GLY 3.7 3.4 + - - -
2324H TRP* 1.3 76.1 - - - +
2326H PRO* 1.3 67.7 - - - +
2328H GLY* 4.5 6.7 - - - +
2329H GLY* 3.4 15.6 + - - -
2426H PHE* 4.8 1.0 - - - -
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Residues in contact with PRO2326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2314H LEU* 3.6 21.8 - - + -
2322H ILE* 4.4 11.4 - - + -
2324H TRP* 3.4 28.7 - - + +
2325H ASN* 1.3 84.1 - - - +
2327H CYS* 1.3 67.5 + - + +
2329H GLY 3.7 0.3 + - - -
2330H GLU* 3.4 20.3 + - - +
2422H ALA* 3.6 40.0 - - + +
2423H ILE* 4.3 4.0 - - + +
2426H PHE* 4.0 9.5 - - + +
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Residues in contact with CYS2327 (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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2314H LEU* 3.6 39.0 - - - -
2326H PRO* 1.3 79.7 - - + +
2328H GLY* 1.3 72.4 + - - +
2330H GLU* 3.3 6.8 + - - +
2331H ARG* 3.2 21.5 + - - +
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Residues in contact with GLY2328 (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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2306H CYS* 4.1 16.3 - - - -
2314H LEU* 6.1 0.2 - - - -
2325H ASN* 4.2 5.1 + - - +
2326H PRO 3.5 0.2 - - - -
2327H CYS* 1.3 85.0 - - - +
2329H GLY* 1.3 57.0 + - - +
2331H ARG* 3.4 7.3 + - - +
2332H TYR* 2.9 30.8 + - - +
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Residues in contact with GLY2329 (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* 6.0 2.7 - - - -
2306H CYS* 4.0 8.6 - - - -
2325H ASN 3.4 13.5 + - - -
2327H CYS 3.2 1.0 - - - -
2328H GLY* 1.3 77.0 - - - +
2330H GLU* 1.3 56.2 + - - +
2332H TYR* 3.3 5.3 + - - +
2333H LEU* 2.9 34.9 + - - +
2426H PHE* 3.6 26.5 - - - -
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Residues in contact with GLU2330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2326H PRO 3.4 11.8 + - - +
2327H CYS* 3.3 10.5 + - - +
2329H GLY* 1.3 75.1 - - - +
2331H ARG* 1.3 58.5 + - - +
2333H LEU* 3.3 5.9 + - - +
2334H ASP* 2.9 43.1 + - - +
2425H SER* 5.5 3.8 - - - +
2426H PHE* 3.9 11.9 - - + +
2429H ALA* 5.0 12.1 - - + -
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Residues in contact with ARG2331 (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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2274H LEU* 3.5 39.8 - - + +
2327H CYS 3.2 15.4 + - - +
2328H GLY* 3.8 8.3 - - - +
2329H GLY 3.3 0.2 - - - -
2330H GLU* 1.3 76.8 - - - +
2332H TYR* 1.3 59.8 + - - +
2334H ASP* 3.9 14.1 + - - +
2335H PHE* 4.1 4.5 + - - +
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Residues in contact with TYR2332 (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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2274H LEU* 5.7 2.5 - - - -
2299H VAL* 4.2 15.7 - - + +
2302H TYR* 5.4 2.7 - - + -
2303H LEU* 4.1 29.9 - - + +
2306H CYS* 5.8 2.7 - - + -
2328H GLY 2.9 17.3 + - - +
2329H GLY* 3.8 5.2 - - - +
2330H GLU 3.2 0.2 - - - -
2331H ARG* 1.3 78.2 - - - +
2333H LEU* 1.3 62.0 + - - +
2335H PHE* 3.6 18.3 + - - +
2336H LEU* 4.2 5.0 + - - +
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Residues in contact with LEU2333 (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* 5.1 11.2 - - + -
2329H GLY 2.9 20.7 + - - +
2330H GLU* 4.0 3.6 - - - +
2332H TYR* 1.3 74.3 - - + +
2334H ASP* 1.3 62.1 + - - +
2335H PHE 3.1 2.2 - - - -
2336H LEU* 3.3 13.2 + - + +
2337H ARG* 2.9 25.2 + - - +
2358H LEU* 5.6 5.8 - - + -
2364H CYS 6.0 1.3 - - - +
2426H PHE* 3.6 28.0 - - + +
2429H ALA* 4.7 9.4 - - + +
2430H LEU* 4.1 39.9 - - + +
2433H LEU* 3.3 30.7 - - + +
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Residues in contact with ASP2334 (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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2274H LEU* 6.0 1.6 - - + -
2278H ALA* 5.2 0.7 - - + -
2330H GLU* 2.9 29.6 + - - +
2331H ARG* 4.1 8.9 - - - +
2332H TYR 3.3 0.4 - - - -
2333H LEU* 1.3 77.5 - - - +
2335H PHE* 1.3 57.5 + - - +
2337H ARG* 3.5 11.0 - - - +
2338H PHE* 2.9 55.3 + - + -
2429H ALA* 4.9 10.2 - - - +
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Residues in contact with PHE2335 (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* 4.6 11.4 - - + -
2259H LEU* 5.8 5.4 - - + -
2274H LEU* 4.4 10.9 - - + +
2277H ALA* 3.7 32.1 - - + -
2278H ALA* 4.0 23.5 - - + +
2281H VAL* 4.1 18.6 - - + +
2291H LEU* 5.8 2.9 - - + -
2295H ASP* 4.9 11.0 - - + -
2296H LEU* 5.0 11.9 - - + -
2299H VAL* 3.7 40.2 - - + -
2331H ARG 4.1 5.1 + - - +
2332H TYR* 3.6 13.9 + - - +
2333H LEU 3.1 0.4 - - - -
2334H ASP* 1.3 78.3 - - - +
2336H LEU* 1.3 63.8 + - + +
2338H PHE* 3.3 2.4 + - - +
2339H ALA* 2.9 34.7 + - + +
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Residues in contact with LEU2336 (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* 3.5 32.5 - - + -
2299H VAL* 3.8 21.3 - - + -
2300H VAL* 3.9 24.0 - - + -
2303H LEU* 6.0 3.1 - - + -
2332H TYR 4.7 6.1 - - - +
2333H LEU* 3.3 13.1 + - + +
2335H PHE* 1.3 82.2 - - + +
2337H ARG* 1.3 56.8 - - - +
2339H ALA* 4.1 4.0 - - + -
2340H VAL* 2.9 39.2 + - + +
2354H VAL* 4.8 11.7 - - + -
2358H LEU* 4.7 9.4 - - + -
2433H LEU* 3.5 32.5 - - + -
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Residues in contact with ARG2337 (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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2333H LEU 2.9 17.8 + - - +
2334H ASP* 3.5 13.5 - - - +
2335H PHE 3.2 0.2 - - - -
2336H LEU* 1.3 76.6 - - - +
2338H PHE* 1.3 86.7 + - + +
2340H VAL* 3.3 17.4 - - - +
2341H PHE* 3.2 46.2 + - - +
2429H ALA 6.0 0.7 - - - +
2432H ASP* 5.3 13.6 + - - +
2433H LEU* 3.9 15.1 - - + +
2436H ARG* 5.1 6.1 - - - -
2505H LEU* 6.3 1.0 - - - +
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Residues in contact with PHE2338 (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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2278H ALA* 3.6 36.1 - - + +
2281H VAL* 4.8 3.7 - - + +
2282H ILE* 3.2 43.2 + - + +
2334H ASP* 2.9 36.0 + - + +
2335H PHE 3.9 2.5 - - - +
2337H ARG* 1.3 103.4 - - + +
2339H ALA* 1.3 59.7 + - - +
2341H PHE* 3.3 10.2 - - - +
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Residues in contact with ALA2339 (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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2281H VAL* 4.0 27.1 - - + +
2288H ALA* 5.3 7.6 - - - +
2291H LEU* 4.9 12.2 - - + +
2296H LEU* 5.2 5.2 - - + -
2335H PHE* 2.9 27.0 + - + +
2336H LEU* 3.1 12.1 + - + +
2338H PHE* 1.3 77.9 - - - +
2340H VAL* 1.3 64.6 + - + +
2341H PHE 3.3 3.7 + - - +
2342H VAL* 5.6 1.9 - - - +
2347H VAL* 6.1 0.7 - - - +
2350H ASN* 5.6 4.7 - - - +
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Residues in contact with VAL2340 (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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2336H LEU* 2.9 24.8 + - + +
2337H ARG* 3.3 16.6 - - - +
2339H ALA* 1.3 77.9 - - + +
2341H PHE* 1.3 61.4 + - + +
2342H VAL* 3.9 2.4 + - - +
2345H GLU 4.4 0.2 - - - +
2346H SER* 3.9 25.5 + - - -
2347H VAL* 4.3 5.2 + - - +
2350H ASN* 5.8 6.5 - - + +
2351H ALA* 5.3 5.4 - - + +
2354H VAL* 4.1 34.3 - - + -
2433H LEU* 5.4 7.2 - - + +
2436H ARG* 3.9 29.4 - - + +
2437H CYS* 4.6 12.8 - - + +
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Residues in contact with PHE2341 (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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2281H VAL 5.6 0.7 - - - +
2282H ILE* 3.7 15.5 - - + +
2337H ARG* 3.2 52.1 + - - +
2338H PHE 3.3 15.7 - - - +
2339H ALA 3.3 2.6 - - - +
2340H VAL* 1.3 81.7 - - + +
2342H VAL* 1.3 61.4 + - - +
2343H ASN 4.3 0.4 - - - -
2344H GLY* 3.3 33.7 - - - +
2345H GLU 4.5 0.4 - - - -
2346H SER* 4.4 9.6 - - - -
2436H ARG* 3.5 31.4 - - + -
2509H ARG* 4.3 22.0 - - - -
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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