Contacts of the helix formed by residues 2423 - 2437 (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 ILE2423 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2322H ILE* 4.1 17.9 - - + -
2324H TRP* 3.5 37.0 - - + -
2326H PRO* 5.1 4.7 - - + -
2380H THR* 5.0 8.7 - - + -
2381H ILE* 5.2 1.1 - - + -
2384H ALA* 4.4 22.2 - - + -
2422H ALA* 1.3 88.1 - - + +
2424H MET* 1.3 61.9 + - - +
2426H PHE* 3.3 2.1 + - - +
2427H TYR* 2.9 50.3 + - + -
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Residues in contact with MET2424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2381H ILE* 4.8 9.9 - - + -
2384H ALA* 5.1 2.8 - - + +
2385H ILE* 3.8 29.8 - - + -
2422H ALA 3.5 1.5 - - - +
2423H ILE* 1.3 80.8 - - - +
2425H SER* 1.3 56.8 + - - +
2427H TYR* 3.4 6.4 + - - +
2428H ALA* 2.9 24.1 + - - +
2495H PHE* 5.5 1.3 - - + -
2499H HIS* 3.1 29.5 - - + +
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Residues in contact with SER2425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2330H GLU* 5.5 4.7 - - - +
2422H ALA* 3.6 22.5 + - - +
2423H ILE 3.3 0.6 - - - -
2424H MET* 1.3 76.2 - - - +
2426H PHE* 1.3 58.3 + - - +
2428H ALA* 3.7 2.5 - - - +
2429H ALA* 2.9 30.5 + - - +
2499H HIS* 3.2 20.6 + - - -
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Residues in contact with PHE2426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2324H TRP* 3.4 40.8 - + + -
2325H ASN 4.9 0.9 - - - -
2326H PRO 4.0 9.6 + - - +
2329H GLY* 3.6 37.7 - - - -
2330H GLU* 3.9 6.2 - - - +
2333H LEU* 3.6 21.1 - - + -
2364H CYS 5.0 9.9 - - - -
2365H PHE 5.6 0.2 - - - -
2366H GLY* 4.9 12.6 - - - -
2367H PRO* 5.8 0.4 - - + -
2422H ALA 3.0 19.6 + - - +
2423H ILE 3.7 2.9 - - - +
2425H SER* 1.3 76.3 - - - +
2427H TYR* 1.3 66.9 + + - +
2429H ALA* 3.3 5.9 + - - +
2430H LEU* 2.9 46.2 + - + +
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Residues in contact with TYR2427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2324H TRP* 4.0 13.4 + + - -
2366H GLY* 4.1 19.5 - - - -
2367H PRO* 4.2 4.6 - - + +
2368H ALA* 3.4 33.8 + - + +
2369H LEU* 4.9 14.4 - - + -
2377H LEU* 5.1 15.3 - - + -
2380H THR* 4.5 9.9 - - + +
2381H ILE* 3.6 28.5 - - + -
2423H ILE* 2.9 47.7 + - + +
2424H MET 3.8 2.9 - - - +
2426H PHE* 1.3 82.6 - + - +
2428H ALA* 1.3 57.8 + - - +
2430H LEU* 3.3 15.6 + - + +
2431H ILE* 2.9 32.0 + - - +
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Residues in contact with ALA2428 (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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2424H MET 2.9 18.2 + - - +
2425H SER* 3.7 4.7 - - - +
2426H PHE 3.3 0.2 - - - -
2427H TYR* 1.3 74.3 - - - +
2429H ALA* 1.3 59.3 + - - +
2431H ILE* 3.1 11.1 - - - +
2432H ASP* 2.9 31.0 + - - +
2499H HIS* 3.6 32.3 - - + +
2502H SER* 4.2 10.5 - - - -
2503H MET* 5.1 3.8 - - - -
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Residues in contact with ALA2429 (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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2330H GLU* 5.0 11.2 - - + -
2333H LEU* 4.7 13.2 - - + +
2334H ASP* 4.9 12.6 - - - +
2337H ARG* 6.0 0.9 - - - +
2425H SER 2.9 16.7 + - - +
2426H PHE* 3.7 6.7 - - - +
2428H ALA* 1.3 75.8 - - - +
2430H LEU* 1.3 58.5 + - - +
2432H ASP* 3.4 5.9 + - - +
2433H LEU* 2.9 30.1 + - - +
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Residues in contact with LEU2430 (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* 4.1 31.1 - - + +
2358H LEU* 5.6 3.8 - - + -
2364H CYS* 4.9 7.9 - - - +
2365H PHE* 4.3 16.2 - - + -
2366H GLY* 3.9 26.0 - - - +
2426H PHE* 2.9 31.3 + - + +
2427H TYR* 3.6 16.4 - - + +
2428H ALA 3.3 0.2 - - - -
2429H ALA* 1.3 76.4 - - - +
2431H ILE* 1.3 58.8 + - - +
2433H LEU* 3.3 3.9 + - + +
2434H LEU* 2.9 53.1 + - + +
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Residues in contact with ILE2431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2377H LEU* 6.0 1.3 - - + -
2427H TYR 2.9 17.6 + - - +
2428H ALA* 3.1 21.8 - - - +
2430H LEU* 1.3 74.1 - - - +
2432H ASP* 1.3 61.4 + - - +
2434H LEU* 3.3 7.5 + - + -
2435H GLY 2.9 24.1 + - - -
2462H VAL* 3.7 27.8 - - + -
2502H SER* 5.0 4.9 - - - +
2503H MET* 4.1 27.8 - - + -
2506H PHE* 3.5 51.1 - - + -
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Residues in contact with ASP2432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2337H ARG* 5.3 13.1 - - - +
2428H ALA 2.9 18.6 + - - +
2429H ALA* 3.7 6.7 - - - +
2431H ILE* 1.3 79.5 - - - +
2433H LEU* 1.3 56.3 + - - +
2435H GLY* 3.4 1.7 + - - -
2436H ARG* 2.9 29.0 + - - +
2502H SER* 4.4 21.1 - - - +
2505H LEU* 6.5 1.6 - - + -
2506H PHE* 5.4 2.0 - - - -
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Residues in contact with LEU2433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2333H LEU* 3.3 52.0 - - + +
2336H LEU* 3.5 30.3 - - + +
2337H ARG* 3.9 16.3 - - + +
2340H VAL* 5.4 6.9 - - + +
2354H VAL* 5.9 4.3 - - + -
2358H LEU* 4.6 12.1 - - + -
2429H ALA 2.9 17.0 + - - +
2430H LEU* 3.6 5.4 - - - +
2432H ASP* 1.3 75.6 - - - +
2434H LEU* 1.3 75.0 + - + +
2436H ARG* 3.2 13.4 + - - +
2437H CYS* 3.1 25.4 + - + +
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Residues in contact with LEU2434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2355H VAL* 5.8 2.2 - - + -
2358H LEU* 3.6 33.7 - - + -
2359H ILE* 6.4 1.3 - - + -
2365H PHE* 3.9 17.7 - - + -
2430H LEU* 2.9 45.6 + - + +
2431H ILE* 3.3 16.8 + - + +
2433H LEU* 1.3 80.5 - - + +
2435H GLY* 1.3 59.4 + - - +
2437H CYS* 3.2 22.4 + - - -
2438H ALA* 4.1 6.8 + - - +
2458H LEU* 4.8 20.6 - - + +
2461H LEU* 5.3 11.7 - - + -
2462H VAL* 5.8 5.6 - - + -
2506H PHE* 4.6 3.8 - - + -
2510H VAL* 4.8 2.1 - - - +
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Residues in contact with GLY2435 (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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2431H ILE 2.9 12.7 + - - -
2432H ASP 3.7 1.8 - - - -
2434H LEU* 1.3 77.6 - - - +
2436H ARG* 1.3 56.5 + - - +
2438H ALA* 3.5 12.4 + - - +
2506H PHE* 3.5 27.5 - - - -
2509H ARG* 2.7 31.4 + - - +
2510H VAL* 3.9 7.9 - - - -
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Residues in contact with ARG2436 (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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2337H ARG* 5.1 2.7 - - - -
2340H VAL* 3.9 18.4 - - + +
2341H PHE* 3.5 31.0 - - + -
2346H SER* 3.5 12.8 + - - -
2432H ASP 2.9 17.7 + - - +
2433H LEU* 3.2 7.8 + - - +
2435H GLY* 1.3 74.1 - - - +
2437H CYS* 1.3 57.3 + - - +
2438H ALA 3.1 5.0 + - - -
2509H ARG* 2.8 29.2 + - - +
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Residues in contact with CYS2437 (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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2340H VAL* 4.6 9.8 - - + +
2346H SER* 5.5 0.7 - - - -
2351H ALA* 3.5 24.5 - - + +
2354H VAL* 4.0 18.8 - - + -
2355H VAL* 3.5 35.3 - - + +
2358H LEU* 5.5 1.8 - - - -
2433H LEU* 3.1 24.9 + - + +
2434H LEU* 3.2 25.6 - - - -
2436H ARG* 1.3 75.5 - - - +
2438H ALA* 1.3 62.1 + - - +
2439H PRO* 3.7 4.5 - - - +
2454H ILE* 5.4 2.3 - - - +
2458H LEU* 4.6 3.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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