Contacts of the helix formed by residues 2423 - 2437 (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 ILE2423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2322B ILE* 4.1 17.3 - - + -
2324B TRP* 3.5 37.0 - - + -
2326B PRO* 5.1 4.5 - - + -
2380B THR* 5.0 9.2 - - + -
2381B ILE* 5.2 1.8 - - + -
2384B ALA* 4.4 20.9 - - + -
2422B ALA* 1.3 88.5 - - + +
2424B MET* 1.3 62.3 + - - +
2426B PHE* 3.3 2.1 + - - +
2427B TYR* 2.9 49.1 + - + -
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Residues in contact with MET2424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2381B ILE* 4.8 9.6 - - + -
2384B ALA* 5.1 3.2 - - + +
2385B ILE* 3.8 29.4 - - + -
2422B ALA 3.5 1.7 - - - +
2423B ILE* 1.3 79.3 - - - +
2425B SER* 1.3 57.6 + - - +
2427B TYR* 3.4 6.0 + - - +
2428B ALA 2.9 24.1 + - - -
2495B PHE* 5.5 2.2 - - + -
2499B HIS* 3.1 28.7 - - + +
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Residues in contact with SER2425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2330B GLU* 5.5 4.4 - - - +
2422B ALA 3.6 22.1 + - - +
2423B ILE 3.3 0.4 - - - -
2424B MET* 1.3 77.7 - - - +
2426B PHE* 1.3 57.5 + - - +
2428B ALA* 3.3 3.2 + - - +
2429B ALA* 2.9 30.1 + - - +
2499B HIS* 3.2 19.8 + - - -
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Residues in contact with PHE2426 (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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2324B TRP* 3.4 39.0 - + + -
2325B ASN 4.9 0.9 - - - -
2326B PRO 4.0 9.2 - - - +
2329B GLY* 3.6 37.0 - - - -
2330B GLU* 3.9 6.9 - - - +
2333B LEU* 3.6 22.0 - - + -
2364B CYS 5.0 10.1 - - - -
2365B PHE 5.6 0.7 - - - -
2366B GLY* 4.9 12.8 - - - -
2367B PRO* 5.8 0.2 - - + -
2422B ALA 3.0 19.8 + - - +
2423B ILE 3.3 2.2 + - - +
2425B SER* 1.3 77.4 - - - +
2427B TYR* 1.3 67.0 + + - +
2429B ALA* 3.3 5.9 + - - +
2430B LEU* 2.9 44.9 + - + +
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Residues in contact with TYR2427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2324B TRP* 4.0 14.0 + + - -
2366B GLY* 4.1 19.9 - - - -
2367B PRO* 4.2 4.3 - - - +
2368B ALA* 3.4 34.0 + - + +
2369B LEU* 4.9 13.7 - - + -
2377B LEU* 5.1 14.8 - - + -
2380B THR* 4.5 9.8 - - + +
2381B ILE* 3.6 30.1 - - + -
2423B ILE* 2.9 47.6 + - + +
2424B MET 3.8 2.2 - - - +
2426B PHE* 1.3 83.5 - + - +
2428B ALA* 1.3 57.4 + - - +
2430B LEU* 3.6 15.2 - - + +
2431B ILE* 2.9 32.7 + - - +
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Residues in contact with ALA2428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2424B MET 2.9 17.9 + - - +
2425B SER* 3.7 4.5 - - - +
2427B TYR* 1.3 75.6 - - - +
2429B ALA* 1.3 60.2 + - - +
2431B ILE* 3.1 11.2 - - - +
2432B ASP* 2.9 30.5 + - - +
2498B ASP 5.5 0.4 - - - +
2499B HIS* 3.6 31.2 - - + +
2502B SER* 4.2 10.9 - - - -
2503B MET* 5.1 4.0 - - - -
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Residues in contact with ALA2429 (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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2330B GLU* 5.0 10.3 - - + -
2333B LEU* 4.7 14.7 - - + +
2334B ASP* 4.9 12.8 - - - +
2337B ARG* 6.0 0.9 - - - +
2425B SER 2.9 17.8 + - - +
2426B PHE* 3.7 7.0 - - - +
2428B ALA* 1.3 75.9 - - - +
2430B LEU* 1.3 56.9 + - - +
2432B ASP* 3.4 6.0 + - - +
2433B LEU* 2.9 31.1 + - - +
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Residues in contact with LEU2430 (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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2333B LEU* 4.1 31.6 - - + +
2358B LEU* 5.6 4.0 - - + -
2364B CYS 4.9 7.4 - - - +
2365B PHE* 4.3 16.6 - - + -
2366B GLY* 3.9 26.5 - - - +
2426B PHE* 2.9 31.4 + - + +
2427B TYR* 3.6 14.6 - - + +
2429B ALA* 1.3 78.3 - - - +
2431B ILE* 1.3 56.5 - - - +
2433B LEU* 3.3 3.4 + - + +
2434B LEU* 2.9 53.1 + - + +
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Residues in contact with ILE2431 (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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2377B LEU* 6.0 1.1 - - + -
2427B TYR 2.9 17.2 + - - +
2428B ALA* 3.1 21.5 - - - +
2430B LEU* 1.3 75.7 - - - +
2432B ASP* 1.3 60.3 + - - +
2434B LEU* 3.3 6.9 + - + -
2435B GLY 2.9 23.7 + - - -
2462B VAL* 3.7 28.0 - - + -
2502B SER* 5.0 4.9 - - - +
2503B MET* 4.1 28.5 - - + -
2506B PHE* 3.5 50.8 - - + -
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Residues in contact with ASP2432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2337B ARG* 5.3 12.9 + - - +
2428B ALA 2.9 18.5 + - - +
2429B ALA* 3.7 6.7 - - - +
2431B ILE* 1.3 77.8 - - - +
2433B LEU* 1.3 57.1 + - - +
2435B GLY* 3.4 2.1 + - - +
2436B ARG* 2.9 29.7 + - - +
2502B SER* 4.4 20.9 - - - +
2505B LEU* 6.5 1.3 - - + -
2506B PHE* 5.4 2.5 - - - +
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Residues in contact with LEU2433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2333B LEU* 3.3 52.0 - - + +
2336B LEU* 3.5 30.1 - - + +
2337B ARG* 3.9 16.3 - - + +
2340B VAL* 5.4 7.4 - - + +
2354B VAL* 5.9 4.0 - - + -
2358B LEU* 4.6 12.8 - - + -
2429B ALA 2.9 16.1 + - - +
2430B LEU* 3.3 5.6 + - - +
2432B ASP* 1.3 75.4 - - - +
2434B LEU* 1.3 75.5 + - + +
2436B ARG* 3.2 13.0 + - - +
2437B CYS* 3.1 25.1 + - + +
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Residues in contact with LEU2434 (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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2355B VAL* 5.8 2.2 - - + -
2358B LEU* 3.6 34.3 - - + -
2359B ILE* 6.4 0.9 - - + -
2365B PHE* 3.9 17.0 - - + -
2430B LEU* 2.9 46.1 + - + +
2431B ILE* 3.7 15.9 - - + +
2433B LEU* 1.3 79.2 - - + +
2435B GLY* 1.3 58.4 + - - +
2437B CYS* 3.2 22.7 + - - -
2438B ALA* 4.1 6.4 + - - +
2458B LEU* 4.8 21.0 - - + +
2461B LEU* 5.3 11.0 - - + -
2462B VAL* 5.8 5.8 - - + -
2506B PHE* 4.6 4.4 - - + -
2510B VAL* 4.8 2.3 - - - +
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Residues in contact with GLY2435 (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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2431B ILE 2.9 12.7 + - - -
2432B ASP* 3.7 1.8 - - - -
2434B LEU* 1.3 76.9 - - - +
2436B ARG* 1.3 55.2 + - - +
2438B ALA* 3.5 13.3 + - - +
2506B PHE* 3.5 28.4 - - - -
2509B ARG* 2.7 32.3 + - - +
2510B VAL* 3.9 7.4 - - - -
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Residues in contact with ARG2436 (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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2337B ARG* 5.1 2.9 - - - -
2340B VAL* 3.9 18.8 - - + +
2341B PHE* 3.5 30.2 - - + -
2346B SER* 3.5 13.0 + - - -
2432B ASP 2.9 17.7 + - - +
2433B LEU* 3.2 8.0 + - - +
2435B GLY* 1.3 73.4 - - - +
2437B CYS* 1.3 57.3 + - - +
2438B ALA 3.1 5.7 + - - -
2509B ARG* 2.8 29.1 + - - +
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Residues in contact with CYS2437 (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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2340B VAL* 4.6 10.3 - - + +
2346B SER* 5.5 1.3 - - - -
2351B ALA* 3.5 24.1 - - + +
2354B VAL* 4.0 18.2 - - + -
2355B VAL* 3.5 33.7 - - + +
2358B LEU* 5.5 2.0 - - - -
2433B LEU* 3.1 24.0 - - - +
2434B LEU* 3.2 25.1 - - - -
2436B ARG* 1.3 76.0 - - - +
2438B ALA* 1.3 61.1 + - - +
2439B PRO* 3.7 5.4 - - - +
2454B ILE* 5.4 2.3 - - - +
2458B LEU* 4.6 2.5 - - - +
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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