Contacts of the helix formed by residues 2347 - 2360 (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 VAL2347 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2285F ASN* 5.1 4.9 - - - +
2288F ALA* 5.1 15.5 - - + +
2289F LEU* 5.5 7.6 - - + +
2340F VAL 4.3 5.5 + - - +
2342F VAL* 3.9 25.4 - - + -
2346F SER* 1.3 74.3 - - - +
2348F GLU* 1.3 62.9 + - - +
2349F GLU* 3.4 21.5 - - - +
2350F ASN* 3.7 26.2 - - + +
2351F ALA* 3.0 31.7 + - - +
3844F ARG* 5.3 3.6 - - - +
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Residues in contact with GLU2348 (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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2346F SER 3.8 2.4 + - - -
2347F VAL* 1.3 75.1 - - - +
2349F GLU* 1.3 71.3 + - + +
2351F ALA* 3.9 2.5 - - - +
2352F ASN* 2.9 30.1 + - - +
2454F ILE* 5.9 1.0 - - - +
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Residues in contact with GLU2349 (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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2289F LEU* 5.9 1.9 - - - +
2347F VAL* 3.4 18.8 - - - +
2348F GLU* 1.3 85.1 - - + +
2350F ASN* 1.3 57.4 + - - +
2352F ASN* 3.3 6.3 + - - +
2353F VAL* 2.9 35.6 + - + +
3843F GLU* 5.5 10.3 - - + +
3844F ARG* 3.6 41.4 + - + +
3847F LYS* 5.1 12.9 - - - +
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Residues in contact with ASN2350 (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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2288F ALA 5.1 9.0 - - - +
2291F LEU* 6.5 0.9 - - + -
2339F ALA 5.6 6.1 - - - +
2340F VAL* 5.8 6.3 - - + +
2347F VAL* 3.7 27.9 - - + +
2348F GLU 3.3 0.2 - - - -
2349F GLU* 1.3 79.4 - - - +
2351F ALA* 1.3 62.3 + - - +
2353F VAL* 3.1 10.0 - - - +
2354F VAL* 2.9 33.0 + - + +
3844F ARG* 4.6 5.9 - - - +
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Residues in contact with ALA2351 (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* 5.3 4.5 - - + +
2346F SER* 5.1 7.6 - - - -
2347F VAL 3.0 21.6 + - - +
2348F GLU* 3.9 2.5 - - - +
2350F ASN* 1.3 74.9 - - - +
2352F ASN* 1.3 62.6 + - - +
2354F VAL* 3.1 12.0 - - - +
2355F VAL* 2.9 29.0 + - - +
2437F CYS* 3.5 30.5 - - - +
2438F ALA 5.7 0.7 - - - -
2439F PRO* 6.2 1.8 - - + -
2454F ILE* 5.7 3.8 - - + -
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Residues in contact with ASN2352 (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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2348F GLU 2.9 18.5 + - - +
2349F GLU* 3.5 8.5 - - - +
2350F ASN 3.2 0.2 - - - -
2351F ALA* 1.3 76.2 - - - +
2353F VAL* 1.3 60.8 + - + +
2355F VAL* 3.1 11.1 - - - +
2356F ARG* 2.9 28.9 + - - +
2454F ILE* 5.0 15.4 - - + +
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Residues in contact with VAL2353 (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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2293F GLU* 5.2 16.2 - - + -
2296F LEU* 5.4 7.2 - - + -
2349F GLU* 2.9 20.2 + - + +
2350F ASN* 3.1 23.8 - - - +
2352F ASN* 1.3 77.6 - - + +
2354F VAL* 1.3 62.0 + - + +
2356F ARG* 3.3 5.9 + - + +
2357F LEU* 2.9 43.3 + - + +
3844F ARG* 4.6 15.0 - - - +
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Residues in contact with VAL2354 (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* 3.8 28.9 - - + -
2300F VAL* 5.5 4.6 - - + +
2336F LEU* 4.8 12.1 - - + -
2339F ALA* 6.3 0.9 - - + -
2340F VAL* 4.1 19.1 - - + -
2350F ASN* 2.9 19.6 + - + +
2351F ALA* 3.1 26.0 - - - +
2353F VAL* 1.3 80.3 - - + +
2355F VAL* 1.3 58.5 + - - +
2357F LEU* 3.5 6.5 + - - +
2358F LEU* 2.9 31.6 + - - +
2433F LEU* 5.9 4.3 - - + -
2437F CYS* 4.0 19.1 - - + -
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Residues in contact with VAL2355 (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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2351F ALA 2.9 21.2 + - - +
2352F ASN* 3.1 24.2 - - - +
2354F VAL* 1.3 77.2 - - - +
2356F ARG* 1.3 57.7 + - - +
2358F LEU* 3.6 8.8 - - + +
2359F ILE* 2.9 41.1 + - + +
2434F LEU* 5.8 2.0 - - + -
2437F CYS* 3.5 39.5 - - + +
2454F ILE* 4.7 23.8 - - + -
2457F ILE* 6.3 2.0 - - + -
2458F LEU* 5.4 10.1 - - + -
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Residues in contact with ARG2356 (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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2352F ASN 2.9 18.6 + - - +
2353F VAL* 3.5 8.5 - - - +
2355F VAL* 1.3 78.4 - - + +
2357F LEU* 1.3 63.3 + - + +
2359F ILE* 3.4 11.1 + - - +
2360F ARG* 2.9 30.2 + - - +
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Residues in contact with LEU2357 (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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2293F GLU* 4.3 11.4 - - + +
2296F LEU* 4.0 16.4 - - + -
2297F GLU* 3.7 37.7 - - + +
2300F VAL* 4.0 27.2 - - + +
2353F VAL* 2.9 27.4 + - + +
2354F VAL* 3.8 4.0 - - - +
2356F ARG* 1.3 78.5 - - + +
2358F LEU* 1.3 60.1 + - - +
2360F ARG* 4.0 15.9 + - + +
2361F LYS* 4.2 7.3 + - - +
2364F CYS* 5.5 0.7 - - - +
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Residues in contact with LEU2358 (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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2300F VAL* 5.0 9.0 - - + -
2333F LEU* 5.6 6.3 - - + -
2336F LEU* 4.7 19.5 - - + -
2354F VAL 2.9 18.9 + - - +
2355F VAL* 3.6 9.9 - - - +
2356F ARG 3.1 0.2 - - - -
2357F LEU* 1.3 77.3 - - - +
2359F ILE* 1.3 62.3 + - + +
2360F ARG 3.2 0.4 - - - -
2361F LYS 3.0 23.7 + - - +
2364F CYS* 3.3 32.7 - - + -
2365F PHE* 3.5 24.9 - - + -
2430F LEU* 5.6 2.5 - - + -
2433F LEU* 4.6 11.9 - - + -
2434F LEU* 3.6 28.0 - - + -
2437F CYS* 5.5 3.1 - - - -
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Residues in contact with ILE2359 (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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131D LEU* 5.5 0.7 - - + -
177D GLU* 6.4 0.9 - - + -
195D PHE* 3.6 55.9 - - + +
2355F VAL* 2.9 30.1 + - + +
2356F ARG* 3.4 14.4 - - - +
2358F LEU* 1.3 75.1 - - + +
2360F ARG* 1.3 64.6 + - - +
2361F LYS* 3.2 5.0 + - - -
2362F PRO* 4.7 2.6 - - - +
2365F PHE* 4.3 19.5 - - + -
2457F ILE* 4.1 26.9 - - + -
2461F LEU* 5.0 8.7 - - + -
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Residues in contact with ARG2360 (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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179D TYR* 6.2 3.1 - - - +
195D PHE* 4.8 11.5 - - - +
2356F ARG 2.9 17.8 + - - +
2357F LEU* 4.0 13.7 - - + +
2358F LEU 3.2 0.8 - - - -
2359F ILE* 1.3 79.2 - - - +
2361F LYS* 1.3 58.6 + - + +
2362F PRO* 3.9 5.9 - - - +
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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