Contacts of the helix formed by residues 2423 - 2437 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2322F ILE* 4.1 17.7 - - + -
2324F TRP* 3.5 36.1 - - + -
2326F PRO* 5.1 5.2 - - + -
2380F THR* 5.0 8.7 - - + -
2381F ILE* 5.2 1.8 - - + -
2384F ALA* 4.4 23.6 - - + -
2422F ALA* 1.3 87.7 - - + +
2424F MET* 1.3 62.6 + - - +
2426F PHE* 3.3 1.4 + - - +
2427F TYR* 2.9 49.9 + - + -
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Residues in contact with MET2424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2381F ILE* 4.8 8.5 - - + +
2384F ALA* 5.1 3.0 - - + +
2385F ILE* 3.8 30.3 - - + -
2422F ALA 4.5 1.3 - - - +
2423F ILE* 1.3 79.5 - - - +
2425F SER* 1.3 58.1 + - - +
2427F TYR* 3.4 6.0 + - - +
2428F ALA 2.9 25.1 + - - -
2495F PHE* 5.5 1.3 - - + -
2499F HIS* 3.1 29.7 - - + +
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Residues in contact with SER2425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2330F GLU* 5.7 4.7 - - - -
2422F ALA* 3.6 22.6 + - - +
2423F ILE 3.3 0.8 - - - -
2424F MET* 1.3 78.5 - - - +
2426F PHE* 1.3 55.9 + - - +
2428F ALA* 3.3 3.1 + - - +
2429F ALA* 2.9 30.9 + - - +
2499F HIS* 3.2 19.3 + - - -
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Residues in contact with PHE2426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2324F TRP* 3.4 39.9 - + + -
2325F ASN 4.9 0.4 - - - -
2326F PRO* 4.0 9.4 - - + +
2329F GLY* 3.6 37.0 - - - -
2330F GLU* 3.9 7.6 - - - +
2333F LEU* 3.6 21.5 - - + -
2364F CYS 5.0 9.9 - - - -
2365F PHE 5.6 0.4 - - - -
2366F GLY* 4.9 13.0 - - - -
2367F PRO* 5.8 0.2 - - + -
2422F ALA 3.0 19.8 + - - +
2423F ILE 3.7 2.7 - - - +
2425F SER* 1.3 76.8 - - - +
2427F TYR* 1.3 67.2 + + - +
2429F ALA* 3.3 6.1 + - - +
2430F LEU* 2.9 45.5 + - + +
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Residues in contact with TYR2427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2324F TRP* 4.0 14.7 + + - -
2366F GLY* 4.1 19.2 - - - -
2367F PRO* 4.2 4.9 - - - +
2368F ALA* 3.4 34.8 + - + +
2369F LEU* 4.9 14.1 - - + -
2377F LEU* 5.1 15.0 - - + -
2380F THR* 4.5 9.2 - - + +
2381F ILE* 3.6 30.7 - - + -
2423F ILE* 2.9 45.6 + - + +
2424F MET 3.8 2.5 - - - +
2426F PHE* 1.3 84.1 - + - +
2428F ALA* 1.3 57.2 + - - +
2430F LEU* 3.3 15.6 + - + +
2431F ILE* 2.9 31.9 + - - +
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Residues in contact with ALA2428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2424F MET 2.9 17.9 + - - +
2425F SER* 3.7 4.3 - - - +
2427F TYR* 1.3 73.6 - - - +
2429F ALA* 1.3 59.9 + - - +
2431F ILE* 3.1 11.5 - - - +
2432F ASP* 2.9 31.6 + - - +
2498F ASP 5.5 0.7 - - - +
2499F HIS* 3.6 31.6 - - + +
2502F SER* 4.2 11.1 - - - -
2503F MET* 5.1 3.8 - - - -
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Residues in contact with ALA2429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2330F GLU* 5.0 10.3 - - + -
2333F LEU* 4.7 14.3 - - + +
2334F ASP* 4.9 12.1 - - - +
2337F ARG* 6.0 0.5 - - - +
2425F SER 2.9 17.3 + - - +
2426F PHE* 3.7 6.5 - - - +
2428F ALA* 1.3 76.3 - - - +
2430F LEU* 1.3 58.0 + - - +
2432F ASP* 3.7 5.6 - - - +
2433F LEU* 2.9 30.8 + - - +
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Residues in contact with LEU2430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2333F LEU* 4.1 31.6 - - + +
2358F LEU* 5.6 3.6 - - + -
2364F CYS* 4.9 8.1 - - - +
2365F PHE* 4.3 15.9 - - + -
2366F GLY* 3.9 26.9 - - - +
2426F PHE* 2.9 30.7 + - + +
2427F TYR* 3.6 16.2 - - + +
2428F ALA 3.3 0.2 - - - -
2429F ALA* 1.3 77.7 - - - +
2431F ILE* 1.3 57.5 + - - +
2433F LEU* 3.3 3.9 + - + +
2434F LEU* 2.9 52.8 + - + +
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Residues in contact with ILE2431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2377F LEU* 6.0 0.9 - - + -
2427F TYR 2.9 17.8 + - - +
2428F ALA* 3.1 21.3 - - - +
2430F LEU* 1.3 75.1 - - - +
2432F ASP* 1.3 60.7 + - - +
2434F LEU* 4.3 6.7 - - + -
2435F GLY 2.9 24.6 + - - -
2462F VAL* 3.7 28.0 - - + -
2502F SER* 5.0 4.3 - - - +
2503F MET* 4.1 27.6 - - + -
2506F PHE* 3.5 50.4 - - + -
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Residues in contact with ASP2432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2337F ARG* 5.3 12.9 - - - +
2341F PHE* 5.5 0.2 - - - -
2428F ALA 2.9 18.5 + - - +
2429F ALA* 3.7 6.5 - - - +
2431F ILE* 1.3 78.1 - - - +
2433F LEU* 1.3 57.7 + - - +
2435F GLY* 3.4 1.8 + - - +
2436F ARG* 2.9 29.7 + - - +
2502F SER* 4.4 20.6 - - - +
2505F LEU* 6.5 1.8 - - + -
2506F PHE* 5.4 2.5 - - - +
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Residues in contact with LEU2433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2333F LEU* 3.3 51.6 - - + +
2336F LEU* 3.5 31.0 - - + +
2337F ARG* 3.9 16.5 - - + +
2340F VAL* 5.4 6.4 - - + +
2354F VAL* 5.9 4.3 - - + -
2358F LEU* 4.6 12.8 - - + -
2429F ALA 2.9 17.1 + - - +
2430F LEU* 3.6 5.6 - - - +
2432F ASP* 1.3 74.8 - - - +
2434F LEU* 1.3 74.4 + - + +
2436F ARG* 3.2 13.2 + - - +
2437F CYS* 3.1 25.2 + - + -
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Residues in contact with LEU2434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2355F VAL* 5.8 2.2 - - + -
2358F LEU* 3.6 34.5 - - + -
2359F ILE* 6.4 0.9 - - + -
2365F PHE* 3.9 17.3 - - + -
2430F LEU* 2.9 46.1 + - + +
2431F ILE* 3.3 16.6 + - + +
2433F LEU* 1.3 80.0 - - + +
2435F GLY* 1.3 57.7 + - - +
2437F CYS* 3.2 22.4 + - - -
2438F ALA* 4.1 6.8 + - - +
2458F LEU* 4.8 21.3 - - + +
2461F LEU* 5.3 11.7 - - + -
2462F VAL* 5.8 6.1 - - + -
2506F PHE* 4.6 4.3 - - + -
2510F VAL* 4.8 1.9 - - - +
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Residues in contact with GLY2435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2431F ILE 2.9 12.5 + - - -
2432F ASP* 3.7 2.5 - - - -
2434F LEU* 1.3 76.4 - - - +
2436F ARG* 1.3 55.4 + - - +
2437F CYS 3.4 0.2 - - - -
2438F ALA* 3.5 12.5 + - - +
2506F PHE* 3.5 28.0 - - - -
2509F ARG* 2.7 31.1 + - - +
2510F VAL* 3.9 8.1 - - - -
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Residues in contact with ARG2436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2337F ARG* 5.1 2.2 - - - -
2340F VAL* 3.9 19.0 - - + +
2341F PHE* 3.5 30.6 - - + -
2346F SER* 3.5 13.3 + - - -
2432F ASP 2.9 16.7 + - - +
2433F LEU* 3.2 8.7 + - - +
2435F GLY* 1.3 74.0 - - - +
2437F CYS* 1.3 57.0 + - - +
2438F ALA 3.1 5.2 + - - +
2509F ARG* 2.8 29.1 + - - +
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Residues in contact with CYS2437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2340F VAL* 4.6 9.8 - - + +
2346F SER* 5.6 0.7 - - - -
2351F ALA* 3.5 25.1 - - + +
2354F VAL* 4.0 18.4 - - + -
2355F VAL* 3.5 33.4 - - + +
2358F LEU* 5.5 2.0 - - - -
2433F LEU* 3.1 25.5 + - + +
2434F LEU* 3.2 25.8 - - - -
2436F ARG* 1.3 76.2 - - - +
2438F ALA* 1.3 62.4 + - - +
2439F PRO* 3.7 4.3 - - - +
2454F ILE* 5.4 2.3 - - - +
2458F LEU* 4.6 2.7 - - - +
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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