Contacts of the helix formed by residues 2325 - 2341 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2306D CYS* 3.8 30.2 + - - +
2307D GLY* 4.4 0.9 - - - -
2311D CYS* 4.2 12.8 - - + -
2314D LEU* 3.7 29.2 - - + -
2322D ILE* 5.3 0.4 - - - -
2323D GLY 3.7 3.2 + - - -
2324D TRP* 1.3 77.9 - - - +
2326D PRO* 1.3 67.3 - - - +
2328D GLY* 4.5 5.8 - - - +
2329D GLY* 3.4 15.8 + - - -
2426D PHE* 4.8 1.0 - - - -
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Residues in contact with PRO2326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2314D LEU* 3.6 22.2 - - + -
2322D ILE* 4.4 11.7 - - + -
2324D TRP* 3.4 28.9 - - + +
2325D ASN* 1.3 83.3 - - - +
2327D CYS* 1.3 66.4 + - + +
2329D GLY 3.7 0.2 + - - -
2330D GLU* 3.4 20.8 + - - +
2422D ALA* 3.6 39.9 - - + +
2423D ILE* 4.3 4.0 - - + +
2426D PHE* 4.0 8.5 - - + +
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Residues in contact with CYS2327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2314D LEU* 3.6 39.3 - - - -
2326D PRO* 1.3 79.7 - - + +
2328D GLY* 1.3 73.2 + - - +
2330D GLU* 3.3 7.0 + - - +
2331D ARG* 3.2 21.2 + - - +
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Residues in contact with GLY2328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2306D CYS* 4.1 16.3 - - - -
2314D LEU* 6.1 0.2 - - - -
2325D ASN* 4.2 5.1 + - - +
2327D CYS* 1.3 86.7 - - - +
2329D GLY* 1.3 56.7 + - - +
2331D ARG* 3.4 7.8 + - - +
2332D TYR* 2.9 30.5 + - - +
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Residues in contact with GLY2329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2303D LEU* 6.0 2.5 - - - -
2306D CYS* 4.0 8.8 - - - -
2325D ASN 3.4 13.3 + - - -
2326D PRO 3.7 0.2 + - - -
2327D CYS 3.2 1.0 - - - -
2328D GLY* 1.3 77.2 - - - +
2330D GLU* 1.3 55.5 + - - +
2332D TYR* 3.3 4.6 + - - +
2333D LEU* 2.9 34.7 + - - +
2426D PHE* 3.6 26.7 - - - -
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Residues in contact with GLU2330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2326D PRO 3.4 11.3 + - - +
2327D CYS* 3.3 8.8 + - - +
2329D GLY* 1.3 75.9 - - - +
2331D ARG* 1.3 57.4 + - - +
2333D LEU* 3.8 5.7 - - - +
2334D ASP* 2.9 42.3 + - - +
2425D SER* 5.5 3.8 - - - +
2426D PHE* 3.9 12.3 - - + +
2429D ALA* 5.0 12.1 - - + -
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Residues in contact with ARG2331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2274D LEU* 3.5 39.1 - - + +
2327D CYS 3.2 15.8 + - - +
2328D GLY* 3.8 8.3 - - - +
2330D GLU* 1.3 77.5 - - - +
2332D TYR* 1.3 61.5 + - - +
2334D ASP* 3.9 14.4 + - - +
2335D PHE* 4.1 4.3 + - - +
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Residues in contact with TYR2332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2274D LEU* 5.7 2.7 - - - -
2299D VAL* 4.2 15.4 - - + +
2302D TYR* 5.4 2.7 - - + -
2303D LEU* 4.1 29.8 - - + +
2306D CYS* 5.8 2.2 - - + -
2328D GLY 2.9 18.3 + - - +
2329D GLY* 3.8 4.7 - - - +
2331D ARG* 1.3 76.9 - - - +
2333D LEU* 1.3 63.0 + - - +
2335D PHE* 3.6 17.9 + - - +
2336D LEU* 4.2 4.9 + - - +
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Residues in contact with LEU2333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2303D LEU* 5.1 12.3 - - + -
2329D GLY* 2.9 21.5 + - - +
2330D GLU* 4.0 4.0 - - - +
2332D TYR* 1.3 74.0 - - + +
2334D ASP* 1.3 61.6 + - - +
2335D PHE 3.1 2.0 - - - -
2336D LEU* 3.3 12.8 + - + +
2337D ARG* 2.9 26.2 + - - +
2358D LEU* 5.6 5.8 - - + -
2364D CYS 6.0 1.3 - - - +
2426D PHE* 3.6 27.1 - - + +
2429D ALA* 4.7 8.7 - - + +
2430D LEU* 4.1 41.7 - - + +
2433D LEU* 3.3 30.3 - - + +
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Residues in contact with ASP2334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2274D LEU* 6.0 2.0 - - + -
2278D ALA* 5.2 0.9 - - + -
2330D GLU* 2.9 29.1 + - - +
2331D ARG* 4.1 10.0 - - - +
2332D TYR 3.3 0.4 - - - -
2333D LEU* 1.3 77.9 - - - +
2335D PHE* 1.3 56.9 + - - +
2337D ARG* 3.5 11.1 - - - +
2338D PHE* 2.9 54.3 + - + -
2429D ALA* 4.9 10.0 - - - +
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Residues in contact with PHE2335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255D LEU* 4.6 11.9 - - + -
2259D LEU* 5.8 5.6 - - + -
2274D LEU* 4.4 11.6 - - + +
2277D ALA* 3.7 31.4 - - + -
2278D ALA* 4.0 22.8 - - + +
2281D VAL* 4.1 19.6 - - + +
2291D LEU* 5.8 2.9 - - + -
2295D ASP* 4.9 9.6 - - + -
2296D LEU* 5.0 11.9 - - + -
2299D VAL* 3.7 38.8 - - + -
2331D ARG 4.1 4.9 + - - +
2332D TYR* 3.6 14.3 + - - +
2333D LEU 3.1 0.8 - - - -
2334D ASP* 1.3 79.8 - - - +
2336D LEU* 1.3 64.0 + - + +
2338D PHE* 3.3 2.6 + - - +
2339D ALA* 2.9 33.9 + - + +
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Residues in contact with LEU2336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2296D LEU* 3.5 32.1 - - + -
2299D VAL* 3.8 20.2 - - + -
2300D VAL* 3.9 24.2 - - + -
2303D LEU* 6.0 2.9 - - + -
2332D TYR 4.7 5.8 - - - +
2333D LEU* 3.3 13.4 + - + +
2335D PHE* 1.3 81.2 - - + +
2337D ARG* 1.3 58.2 + - - +
2339D ALA* 4.1 4.7 - - + -
2340D VAL* 2.9 38.9 + - + +
2354D VAL* 4.8 12.1 - - + -
2358D LEU* 4.7 9.4 - - + -
2433D LEU* 3.5 31.6 - - + -
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Residues in contact with ARG2337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2333D LEU 2.9 17.9 + - - +
2334D ASP* 3.5 13.7 - - - +
2335D PHE 3.2 0.2 - - - -
2336D LEU* 1.3 76.6 - - - +
2338D PHE* 1.3 87.0 + - + +
2340D VAL* 3.3 16.5 - - - +
2341D PHE* 3.2 45.8 + - - +
2429D ALA 6.0 0.9 - - - +
2432D ASP* 5.3 13.3 - - - +
2433D LEU* 3.9 14.5 - - + +
2436D ARG* 5.1 6.1 - - - -
2505D LEU* 6.3 0.8 - - - +
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Residues in contact with PHE2338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2278D ALA* 3.6 35.2 - - + +
2281D VAL* 4.8 3.5 - - + +
2282D ILE* 3.2 43.5 + - + +
2334D ASP* 2.9 35.6 + - + +
2335D PHE 3.9 3.1 - - - +
2337D ARG* 1.3 103.1 - - + +
2339D ALA* 1.3 59.7 + - - +
2341D PHE* 3.3 10.4 - - - +
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Residues in contact with ALA2339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281D VAL* 4.0 26.1 - - + +
2288D ALA* 5.3 7.8 - - - +
2291D LEU* 4.9 11.5 - - + +
2296D LEU* 5.2 4.9 - - + -
2335D PHE* 2.9 28.3 + - + +
2336D LEU* 3.1 11.9 + - + +
2338D PHE* 1.3 77.4 - - - +
2340D VAL* 1.3 65.0 + - + +
2341D PHE 3.5 3.5 + - - +
2342D VAL* 5.6 1.9 - - - +
2347D VAL* 6.1 0.7 - - - +
2350D ASN* 5.6 4.7 - - - +
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Residues in contact with VAL2340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2336D LEU* 2.9 24.3 + - + +
2337D ARG* 3.3 16.6 - - - +
2339D ALA* 1.3 78.1 - - + +
2341D PHE* 1.3 59.6 + - + +
2342D VAL* 3.9 2.0 + - - +
2346D SER* 3.9 26.1 + - - +
2347D VAL* 4.3 5.2 + - - +
2350D ASN* 5.6 6.4 - - + +
2351D ALA* 5.3 5.2 - - + +
2354D VAL* 4.1 33.9 - - + -
2433D LEU* 5.4 7.0 - - + +
2436D ARG* 3.9 29.8 - - + +
2437D CYS* 4.6 13.0 - - + +
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Residues in contact with PHE2341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281D VAL 5.6 0.9 - - - +
2282D ILE* 3.7 14.7 - - + +
2337D ARG* 3.2 53.0 + - - +
2338D PHE 3.3 16.2 - - - +
2339D ALA 3.3 2.4 - - - +
2340D VAL* 1.3 81.8 - - + +
2342D VAL* 1.3 61.1 + - - +
2343D ASN 4.3 0.4 - - - -
2344D GLY* 3.3 34.8 - - - +
2346D SER* 4.4 9.4 - - - -
2436D ARG* 3.5 31.4 - - + -
2509D ARG* 4.3 22.4 - - - -
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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