Contacts of the helix formed by residues 2325 - 2341 (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 ASN2325 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2306F CYS* 3.8 28.8 + - - +
2307F GLY* 4.4 1.9 - - - -
2311F CYS* 4.2 13.0 - - + +
2314F LEU* 3.7 30.1 - - + -
2322F ILE* 5.3 0.4 - - - -
2323F GLY 3.7 3.4 + - - -
2324F TRP* 1.3 76.8 - - - +
2326F PRO* 1.3 68.2 - - - +
2328F GLY* 4.5 6.5 - - - +
2329F GLY* 3.4 15.9 + - - -
2426F PHE* 4.8 0.9 - - - -
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Residues in contact with PRO2326 (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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2314F LEU* 3.7 20.2 - - + -
2322F ILE* 4.4 12.3 - - + -
2324F TRP* 3.4 28.7 - - + +
2325F ASN* 1.3 83.1 - - - +
2327F CYS* 1.3 68.2 + - + +
2329F GLY 3.7 0.5 + - - -
2330F GLU* 3.4 19.9 + - - +
2422F ALA* 3.6 40.1 - - + +
2423F ILE* 4.3 3.8 - - + +
2426F PHE* 4.0 8.5 - - + +
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Residues in contact with CYS2327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2314F LEU* 3.6 38.8 - - - -
2326F PRO* 1.3 79.3 - - + +
2328F GLY* 1.3 73.8 + - - +
2330F GLU* 3.3 7.2 + - - +
2331F ARG* 3.2 20.6 + - - +
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Residues in contact with GLY2328 (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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2306F CYS* 4.1 15.4 - - - -
2325F ASN* 4.2 4.9 + - - +
2327F CYS* 1.3 86.5 - - - +
2329F GLY* 1.3 56.3 + - - +
2331F ARG* 3.4 7.7 + - - +
2332F TYR* 2.9 30.8 + - - +
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Residues in contact with GLY2329 (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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2303F LEU* 6.0 2.2 - - - -
2306F CYS* 4.0 8.1 - - - -
2325F ASN 3.4 13.9 + - - -
2326F PRO 3.7 0.2 + - - -
2327F CYS 3.2 1.2 - - - -
2328F GLY* 1.3 78.5 - - - +
2330F GLU* 1.3 55.7 + - - +
2332F TYR* 3.3 5.2 + - - +
2333F LEU* 2.9 34.1 + - - +
2426F PHE* 3.6 26.5 - - - -
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Residues in contact with GLU2330 (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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2326F PRO 3.4 11.1 + - - +
2327F CYS* 3.3 9.9 + - - +
2329F GLY* 1.3 74.9 - - - +
2331F ARG* 1.3 59.1 + - - +
2333F LEU* 3.8 5.6 - - - -
2334F ASP* 2.9 43.3 + - - +
2425F SER* 5.5 3.1 - - - +
2426F PHE* 3.9 12.6 - - + +
2429F ALA* 5.0 11.9 - - + -
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Residues in contact with ARG2331 (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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2274F LEU* 3.5 39.9 - - + +
2327F CYS 3.2 15.0 + - - +
2328F GLY* 3.8 8.3 - - - +
2330F GLU* 1.3 77.1 - - - +
2332F TYR* 1.3 60.9 + - - +
2334F ASP* 3.9 14.6 + - - +
2335F PHE* 4.1 4.3 + - - +
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Residues in contact with TYR2332 (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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2274F LEU* 5.7 2.5 - - - -
2299F VAL* 4.2 14.4 - - + +
2302F TYR* 5.4 2.9 - - + -
2303F LEU* 4.1 31.0 - - + +
2306F CYS* 5.8 1.8 - - + -
2328F GLY 2.9 18.1 + - - +
2329F GLY* 3.8 5.6 - - - +
2331F ARG* 1.3 77.7 - - - +
2333F LEU* 1.3 61.2 + - - +
2335F PHE* 3.6 18.1 + - - +
2336F LEU* 4.2 5.4 + - - +
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Residues in contact with LEU2333 (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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2303F LEU* 5.1 11.4 - - + -
2329F GLY 2.9 20.2 + - - +
2330F GLU* 4.0 4.0 - - - +
2332F TYR* 1.3 74.3 - - + +
2334F ASP* 1.3 62.7 + - - +
2335F PHE 3.1 2.2 - - - -
2336F LEU* 3.3 13.5 + - + +
2337F ARG* 2.9 24.5 + - - +
2358F LEU* 5.6 6.3 - - + -
2364F CYS 6.0 1.6 - - - +
2426F PHE* 3.6 27.6 - - + +
2429F ALA* 4.7 9.0 - - + +
2430F LEU* 4.1 40.4 - - + +
2433F LEU* 3.3 31.5 - - + +
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Residues in contact with ASP2334 (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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2274F LEU* 6.0 1.6 - - + -
2278F ALA* 5.2 0.7 - - + -
2330F GLU* 2.9 29.7 + - - +
2331F ARG* 4.1 10.1 - - - +
2332F TYR 3.3 0.2 - - - -
2333F LEU* 1.3 77.8 - - - +
2335F PHE* 1.3 56.6 + - - +
2337F ARG* 3.5 10.6 - - - +
2338F PHE* 2.9 54.3 + - + -
2429F ALA* 4.9 9.9 - - - +
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Residues in contact with PHE2335 (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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2255F LEU* 4.6 11.4 - - + -
2259F LEU* 5.8 5.6 - - + -
2274F LEU* 4.4 10.9 - - + +
2277F ALA* 3.7 31.9 - - + -
2278F ALA* 4.0 24.2 - - + +
2281F VAL* 4.1 18.7 - - + +
2291F LEU* 5.8 3.1 - - + -
2295F ASP* 4.9 10.5 - - + -
2296F LEU* 5.0 11.4 - - + -
2299F VAL* 3.7 39.5 - - + -
2331F ARG 4.1 4.7 + - - +
2332F TYR* 3.6 13.9 + - - +
2333F LEU 3.1 0.2 - - - -
2334F ASP* 1.3 79.4 - - - +
2336F LEU* 1.3 64.3 + - + +
2338F PHE* 3.3 2.6 + - - +
2339F ALA* 2.9 33.9 + - + +
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Residues in contact with LEU2336 (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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2296F LEU* 3.5 32.3 - - + -
2299F VAL* 3.8 20.9 - - + -
2300F VAL* 3.9 24.2 - - + -
2303F LEU* 6.0 3.4 - - + -
2332F TYR 4.7 5.4 - - - +
2333F LEU* 3.3 12.7 + - + +
2335F PHE* 1.3 80.7 - - + +
2337F ARG* 1.3 56.2 + - - +
2339F ALA* 4.1 4.0 - - + -
2340F VAL* 2.9 38.8 + - + +
2354F VAL* 4.8 12.1 - - + -
2358F LEU* 4.7 9.6 - - + -
2433F LEU* 3.5 32.3 - - + -
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Residues in contact with ARG2337 (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 2.9 17.8 + - - +
2334F ASP* 3.5 13.2 - - - +
2336F LEU* 1.3 77.7 - - - +
2338F PHE* 1.3 86.2 + - + +
2340F VAL* 3.3 17.4 - - - +
2341F PHE* 3.2 45.4 + - - +
2429F ALA 6.0 0.4 - - - +
2432F ASP* 5.3 13.3 + - - +
2433F LEU* 3.9 15.7 - - + +
2436F ARG* 5.1 5.8 - - - -
2505F LEU* 6.3 1.2 - - - +
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Residues in contact with PHE2338 (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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2278F ALA* 3.6 36.3 - - + +
2281F VAL* 4.8 2.8 - - - +
2282F ILE* 3.2 44.3 + - + +
2334F ASP* 2.9 35.2 + - + +
2335F PHE 3.9 2.7 - - - +
2337F ARG* 1.3 104.9 - - + +
2339F ALA* 1.3 58.6 + - - +
2340F VAL 3.5 0.2 - - - -
2341F PHE* 3.3 10.0 - - - +
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Residues in contact with ALA2339 (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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2281F VAL* 4.0 27.1 - - + +
2288F ALA* 5.3 7.6 - - - +
2291F LEU* 4.9 11.1 - - + +
2296F LEU* 5.2 4.9 - - + -
2335F PHE* 2.9 27.0 + - + +
2336F LEU* 3.1 11.8 + - + +
2338F PHE* 1.3 77.4 - - - +
2340F VAL* 1.3 65.6 + - + +
2341F PHE 3.5 3.5 + - - +
2342F VAL* 5.6 2.1 - - - +
2347F VAL* 6.1 0.5 - - - +
2350F ASN* 5.6 4.2 - - - +
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Residues in contact with VAL2340 (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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2336F LEU* 2.9 24.5 + - + +
2337F ARG* 3.3 17.0 - - - +
2339F ALA* 1.3 78.9 - - + +
2341F PHE* 1.3 60.6 + - + +
2342F VAL* 3.9 2.1 + - - +
2346F SER* 3.9 25.7 + - - -
2347F VAL* 4.3 5.0 + - - +
2350F ASN* 5.8 6.2 - - + +
2351F ALA* 5.3 5.4 - - + +
2354F VAL* 4.1 34.3 - - + -
2433F LEU* 5.4 6.3 - - + +
2436F ARG* 3.9 28.7 - - + +
2437F CYS* 4.6 12.3 - - + +
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Residues in contact with PHE2341 (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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2281F VAL 5.6 0.5 - - - +
2282F ILE* 3.7 14.6 - - + +
2337F ARG* 3.2 52.5 + - - +
2338F PHE 3.3 15.5 - - - +
2339F ALA 3.3 2.9 - - - +
2340F VAL* 1.3 82.9 - - + +
2342F VAL* 1.3 60.9 + - - +
2343F ASN 4.3 0.4 - - - -
2344F GLY* 3.3 35.0 - - - +
2345F GLU 4.5 0.2 - - - -
2346F SER* 4.4 9.0 - - - -
2436F ARG* 3.5 31.4 - - + -
2509F ARG* 4.3 22.2 - - - -
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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