Contacts of the helix formed by residues 2347 - 2360 (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 VAL2347 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2285H ASN* 5.1 4.9 - - - +
2288H ALA* 5.1 15.7 - - + +
2289H LEU* 5.5 7.4 - - + +
2340H VAL 4.3 5.1 + - - +
2342H VAL* 3.9 24.7 - - + -
2346H SER* 1.3 74.4 - - - +
2348H GLU* 1.3 63.4 + - - +
2349H GLU* 3.4 22.7 - - - +
2350H ASN* 3.7 26.7 - - + +
2351H ALA* 3.0 31.4 + - - +
3844H ARG* 5.3 3.1 - - - +
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Residues in contact with GLU2348 (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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2346H SER 3.8 2.4 + - - -
2347H VAL* 1.3 76.0 - - - +
2349H GLU* 1.3 71.3 + - + +
2351H ALA* 3.8 2.9 - - - +
2352H ASN* 2.9 30.4 + - - +
2454H ILE* 5.9 1.0 - - - +
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Residues in contact with GLU2349 (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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2289H LEU* 5.9 1.9 - - - +
2347H VAL* 3.4 18.3 - - - +
2348H GLU* 1.3 85.3 - - + +
2350H ASN* 1.3 57.5 + - - +
2352H ASN* 3.3 6.8 + - - +
2353H VAL* 2.9 35.0 + - + +
3843H GLU* 5.5 10.3 - - + +
3844H ARG* 3.6 42.0 + - + +
3847H LYS* 5.1 12.4 - - - +
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Residues in contact with ASN2350 (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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2288H ALA 5.1 9.2 - - - +
2291H LEU* 6.5 1.1 - - + -
2339H ALA 5.6 6.1 - - - +
2340H VAL* 5.8 6.5 - - + +
2347H VAL* 3.7 27.6 - - + +
2348H GLU 3.3 0.4 - - - -
2349H GLU* 1.3 79.4 - - - +
2351H ALA* 1.3 62.7 + - - +
2353H VAL* 3.1 10.2 - - - +
2354H VAL* 2.9 34.3 + - + +
3844H ARG* 4.6 6.4 - - - +
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Residues in contact with ALA2351 (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* 5.3 5.1 - - + +
2346H SER* 5.1 7.9 - - - -
2347H VAL 3.0 20.5 + - - +
2348H GLU* 3.9 3.6 - - - +
2350H ASN* 1.3 76.0 - - - +
2352H ASN* 1.3 63.5 + - - +
2354H VAL* 3.1 11.2 - - - +
2355H VAL* 2.9 28.6 + - - +
2437H CYS* 3.5 30.5 - - - +
2438H ALA 5.7 0.7 - - - -
2439H PRO* 6.0 2.2 - - + -
2454H ILE* 5.7 3.6 - - + -
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Residues in contact with ASN2352 (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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2348H GLU 2.9 18.6 + - - +
2349H GLU* 3.5 8.3 - - - +
2350H ASN 3.2 0.2 - - - -
2351H ALA* 1.3 75.9 - - - +
2353H VAL* 1.3 59.2 + - + +
2355H VAL* 3.1 12.0 - - - +
2356H ARG* 2.9 29.7 + - - +
2454H ILE* 5.0 14.5 - - + +
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Residues in contact with VAL2353 (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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2293H GLU* 5.2 15.7 - - + -
2296H LEU* 5.4 7.2 - - + -
2349H GLU* 2.9 21.1 + - + +
2350H ASN* 3.1 23.6 - - - +
2352H ASN* 1.3 78.4 - - + +
2354H VAL* 1.3 61.6 + - + +
2356H ARG* 3.5 6.6 - - + +
2357H LEU* 2.9 44.1 + - + +
3844H ARG* 4.6 14.6 - - - +
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Residues in contact with VAL2354 (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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2296H LEU* 3.8 28.3 - - + -
2300H VAL* 5.5 3.6 - - + +
2336H LEU* 4.8 11.7 - - + -
2339H ALA* 6.3 1.1 - - + -
2340H VAL* 4.1 20.0 - - + -
2350H ASN* 2.9 18.9 + - + +
2351H ALA* 3.1 26.7 - - - +
2353H VAL* 1.3 81.6 - - + +
2355H VAL* 1.3 55.8 + - - +
2357H LEU* 3.8 5.9 - - - +
2358H LEU* 2.9 32.8 + - - +
2433H LEU* 5.9 4.3 - - + -
2437H CYS* 4.0 17.9 - - + -
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Residues in contact with VAL2355 (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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2351H ALA 2.9 20.7 + - - +
2352H ASN* 3.1 24.0 - - - +
2354H VAL* 1.3 76.0 - - - +
2356H ARG* 1.3 58.0 + - + +
2358H LEU* 3.6 8.9 - - + +
2359H ILE* 2.9 42.3 + - + +
2434H LEU* 5.8 2.2 - - + -
2437H CYS* 3.5 39.0 - - + +
2454H ILE* 4.7 23.3 - - + -
2457H ILE* 6.3 2.2 - - + -
2458H LEU* 5.4 11.4 - - + -
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Residues in contact with ARG2356 (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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2352H ASN 2.9 18.6 + - - +
2353H VAL* 3.5 8.5 - - + +
2354H VAL 3.2 0.2 - - - -
2355H VAL* 1.3 79.1 - - - +
2357H LEU* 1.3 63.1 + - + +
2359H ILE* 3.4 11.1 - - - +
2360H ARG* 2.9 31.0 + - - +
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Residues in contact with LEU2357 (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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2293H GLU* 4.3 11.4 - - + +
2296H LEU* 4.0 15.9 - - + +
2297H GLU* 3.7 36.1 - - + +
2300H VAL* 4.0 28.8 - - + +
2353H VAL* 2.9 27.8 + - + +
2354H VAL* 4.2 3.8 - - - +
2356H ARG* 1.3 80.2 - - + +
2358H LEU* 1.3 59.7 + - - +
2360H ARG* 4.0 15.0 + - + +
2361H LYS* 4.2 7.4 + - - +
2364H CYS* 5.5 0.7 - - - +
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Residues in contact with LEU2358 (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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2300H VAL* 5.0 8.5 - - + -
2333H LEU* 5.6 7.0 - - + -
2336H LEU* 4.7 19.3 - - + -
2354H VAL 2.9 19.5 + - - +
2355H VAL* 3.6 9.4 - - - +
2356H ARG 3.1 0.4 - - - -
2357H LEU* 1.3 77.0 - - - +
2359H ILE* 1.3 62.0 + - + +
2360H ARG 3.4 0.2 + - - -
2361H LYS 3.0 23.6 + - - +
2364H CYS* 3.3 33.5 - - + -
2365H PHE* 3.5 25.7 - - + -
2430H LEU* 5.9 2.0 - - + -
2433H LEU* 4.6 12.1 - - + -
2434H LEU* 3.6 27.8 - - + -
2437H CYS* 5.5 3.1 - - - -
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Residues in contact with ILE2359 (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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131F LEU* 5.5 0.4 - - + -
177F GLU* 6.4 0.4 - - + -
195F PHE* 3.6 55.8 - - + +
2355H VAL* 2.9 29.8 + - + +
2356H ARG* 3.4 13.7 - - - +
2358H LEU* 1.3 76.2 - - + +
2360H ARG* 1.3 65.2 + - - +
2361H LYS* 3.2 4.9 + - - -
2362H PRO* 4.7 2.8 - - - +
2365H PHE* 4.3 18.8 - - + -
2457H ILE* 4.1 26.9 - - + -
2461H LEU* 5.0 8.5 - - + -
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Residues in contact with ARG2360 (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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179F TYR* 6.2 2.9 - - - +
195F PHE* 4.8 11.5 - - - +
2356H ARG 2.9 19.1 + - - +
2357H LEU* 4.0 13.9 - - + +
2358H LEU 3.2 0.6 - - - -
2359H ILE* 1.3 80.6 - - - +
2361H LYS* 1.3 58.1 + - + +
2362H PRO* 3.9 6.1 - - - +
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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
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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