Contacts of the helix formed by residues 2347 - 2360 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2285B ASN* 5.1 4.9 - - - +
2288B ALA* 5.1 15.9 - - + +
2289B LEU* 5.5 7.4 - - + +
2340B VAL 4.3 5.1 + - - +
2342B VAL* 3.9 25.6 - - + -
2346B SER* 1.3 73.6 - - - +
2348B GLU* 1.3 63.2 + - - +
2349B GLU* 3.4 21.8 - - - +
2350B ASN* 3.7 26.4 - - + +
2351B ALA* 3.0 31.5 + - - +
3844B ARG* 5.3 3.6 - - - +
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Residues in contact with GLU2348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2346B SER 3.8 2.4 + - - -
2347B VAL* 1.3 76.0 - - - +
2349B GLU* 1.3 72.1 + - + +
2351B ALA* 3.4 2.7 + - - +
2352B ASN* 2.9 29.9 + - - +
2454B ILE* 5.9 0.9 - - - +
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Residues in contact with GLU2349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2289B LEU* 5.9 2.1 - - - +
2347B VAL* 3.4 18.4 - - - +
2348B GLU* 1.3 84.0 - - + +
2350B ASN* 1.3 56.3 + - - +
2352B ASN* 3.3 6.6 + - - +
2353B VAL* 2.9 36.2 + - + +
3843B GLU* 5.5 10.1 - - + +
3844B ARG* 3.6 40.7 + - + +
3847B LYS* 5.1 12.9 - - - +
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Residues in contact with ASN2350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2288B ALA 5.1 8.7 - - - +
2291B LEU* 6.5 1.1 - - + -
2339B ALA 5.6 6.1 - - - +
2340B VAL* 5.8 5.8 - - + -
2347B VAL* 3.7 29.2 - - + +
2348B GLU 3.3 0.6 - - - -
2349B GLU* 1.3 79.0 - - - +
2351B ALA* 1.3 62.4 + - - +
2353B VAL* 3.1 9.5 - - - +
2354B VAL* 2.9 33.5 + - + +
3844B ARG* 4.6 6.4 - - - +
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Residues in contact with ALA2351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2340B VAL* 5.3 4.7 - - + +
2346B SER* 5.1 7.4 - - - -
2347B VAL 3.0 20.5 + - - +
2348B GLU* 3.9 3.1 - - - +
2350B ASN* 1.3 76.7 - - - +
2352B ASN* 1.3 63.4 + - - +
2354B VAL* 3.1 10.4 - - - +
2355B VAL* 2.9 29.1 + - - +
2437B CYS* 3.5 31.2 - - - +
2438B ALA 5.7 0.7 - - - -
2439B PRO* 6.0 1.6 - - + -
2454B ILE* 5.7 3.4 - - + -
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Residues in contact with ASN2352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2348B GLU 2.9 17.5 + - - +
2349B GLU* 3.5 9.0 - - - +
2351B ALA* 1.3 77.1 - - - +
2353B VAL* 1.3 59.8 + - + +
2355B VAL* 3.1 11.7 - - - +
2356B ARG* 2.9 29.2 + - - +
2454B ILE* 5.0 15.4 - - + +
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Residues in contact with VAL2353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2293B GLU* 5.2 16.6 - - + -
2296B LEU* 5.4 7.2 - - + -
2349B GLU* 2.9 20.6 + - + +
2350B ASN* 3.1 23.6 - - - +
2352B ASN* 1.3 77.6 - - + +
2354B VAL* 1.3 61.8 + - + +
2356B ARG* 3.3 6.8 + - + +
2357B LEU* 2.9 43.7 + - + +
3844B ARG* 4.6 15.0 - - - +
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Residues in contact with VAL2354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2296B LEU* 3.8 28.3 - - + -
2300B VAL* 5.5 4.5 - - + +
2336B LEU* 4.8 11.2 - - + -
2339B ALA* 6.3 1.3 - - + -
2340B VAL* 4.1 19.7 - - + -
2350B ASN* 2.9 20.0 + - + +
2351B ALA* 3.1 26.7 - - - +
2353B VAL* 1.3 80.4 - - + +
2355B VAL* 1.3 56.7 + - + +
2357B LEU* 3.5 6.1 + - - +
2358B LEU* 2.9 32.4 + - - +
2433B LEU* 5.9 4.0 - - + -
2437B CYS* 4.0 18.2 - - + -
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Residues in contact with VAL2355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2351B ALA 2.9 20.4 + - - +
2352B ASN* 3.1 24.2 - - - +
2354B VAL* 1.3 76.6 - - - +
2356B ARG* 1.3 57.5 + - - +
2358B LEU* 3.6 9.2 - - + +
2359B ILE* 2.9 41.3 + - + +
2434B LEU* 5.8 2.2 - - + -
2437B CYS* 3.5 39.5 - - + +
2454B ILE* 4.7 23.6 - - + -
2457B ILE* 6.3 2.2 - - + -
2458B LEU* 5.4 11.2 - - + -
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Residues in contact with ARG2356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2352B ASN 2.9 18.5 + - - +
2353B VAL* 3.5 9.0 - - + +
2354B VAL 3.2 0.4 - - - -
2355B VAL* 1.3 77.1 - - + +
2357B LEU* 1.3 64.1 + - + +
2358B LEU 3.2 0.3 + - - -
2359B ILE* 3.4 12.0 - - - +
2360B ARG* 2.9 30.4 + - - +
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Residues in contact with LEU2357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2293B GLU* 4.3 12.3 - - + +
2296B LEU* 4.0 15.5 - - + -
2297B GLU* 3.7 37.7 - - + +
2300B VAL* 4.0 27.9 - - + +
2353B VAL* 2.9 29.0 + - + +
2354B VAL* 4.2 3.8 - - - +
2356B ARG* 1.3 78.0 - - + +
2358B LEU* 1.3 59.5 + - - +
2360B ARG* 4.0 15.9 + - + +
2361B LYS* 4.2 7.8 + - - +
2364B CYS* 5.5 0.9 - - - +
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Residues in contact with LEU2358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300B VAL* 5.0 8.7 - - + -
2333B LEU* 5.6 7.0 - - + -
2336B LEU* 4.7 19.1 - - + -
2354B VAL 2.9 19.3 + - - +
2355B VAL* 3.6 9.6 - - + +
2356B ARG 3.1 0.4 - - - -
2357B LEU* 1.3 77.4 - - - +
2359B ILE* 1.3 62.2 + - + +
2360B ARG 3.4 0.2 + - - -
2361B LYS 3.0 23.6 + - - +
2364B CYS* 3.3 34.3 - - + +
2365B PHE* 3.5 24.8 - - + -
2430B LEU* 5.9 2.5 - - + -
2433B LEU* 4.6 12.8 - - + -
2434B LEU* 3.6 27.6 - - + -
2437B CYS* 5.5 3.1 - - - -
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Residues in contact with ILE2359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2355B VAL* 2.9 29.8 + - + +
2356B ARG* 3.4 13.5 - - - +
2358B LEU* 1.3 74.7 - - + +
2360B ARG* 1.3 63.4 + - - +
2361B LYS* 3.2 5.5 + - - -
2362B PRO* 4.7 2.8 - - - +
2365B PHE* 4.3 19.1 - - + -
2457B ILE* 4.1 27.4 - - + -
2461B LEU* 5.0 9.4 - - + -
131H LEU* 5.5 0.4 - - + -
177H GLU* 6.4 0.7 - - + -
195H PHE* 3.6 55.4 - - + +
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Residues in contact with ARG2360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2356B ARG 2.9 17.6 + - - +
2357B LEU* 4.0 14.6 - - + +
2358B LEU 3.2 0.6 - - - -
2359B ILE* 1.3 80.3 - - - +
2361B LYS* 1.3 56.7 + - + +
2362B PRO* 3.9 6.1 - - - +
179H TYR* 6.2 3.1 - - - +
195H PHE* 4.8 12.3 - - - +
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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