Contacts of the helix formed by residues 2295 - 2307 (chain B) in PDB entry 1WUE
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 SER2295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2013B LEU* 4.8 3.6 - - - -
2031B PHE* 3.4 35.8 - - - -
2033B LEU* 4.1 0.2 - - - +
2047B GLU* 2.7 26.1 + - - -
2294B GLU* 1.3 74.9 - - - +
2296B GLY* 1.3 65.5 + - - +
2297B VAL* 3.1 10.9 + - - +
2298B GLY 3.3 0.9 + - - -
2299B ARG* 2.9 25.6 + - - +
2320B THR* 5.3 0.2 - - - -
2324B PHE* 5.0 5.8 - - - -
2327B ASP* 3.9 3.8 - - - -
2328B ILE* 3.5 16.8 - - - +
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Residues in contact with GLY2296 (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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2295B SER* 1.3 73.1 - - - +
2297B VAL* 1.3 56.6 + - - +
2299B ARG* 3.8 2.0 - - - -
2300B ALA* 2.9 32.1 + - - +
2327B ASP* 2.9 36.0 + - - -
2328B ILE* 4.4 0.2 - - - +
2329B ILE* 3.8 10.8 - - - -
2333B PHE* 3.3 19.3 - - - -
2350B VAL* 4.2 1.2 - - - +
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Residues in contact with VAL2297 (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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2033B LEU* 4.3 9.4 - - + -
2045B PHE* 4.0 18.2 - - + +
2046B GLY* 4.2 23.3 - - - +
2047B GLU* 3.9 4.5 - - + +
2295B SER* 3.1 7.5 - - - +
2296B GLY* 1.3 77.8 - - - +
2298B GLY* 1.3 62.0 + - - +
2300B ALA* 3.5 8.0 + - - +
2301B LEU* 3.5 10.9 + - - +
2328B ILE* 3.8 14.1 - - + -
2329B ILE* 4.0 6.0 - - + +
2348B ILE* 3.9 24.5 - - + +
2350B VAL* 4.5 4.7 - - + -
2352B LEU* 3.8 28.9 - - + -
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Residues in contact with GLY2298 (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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2047B GLU* 3.0 25.5 + - - -
2049B VAL* 5.8 0.7 - - - -
2294B GLU* 4.0 15.5 - - - -
2295B SER 3.3 0.4 + - - -
2297B VAL* 1.3 74.0 - - - +
2299B ARG* 1.3 60.0 + - - +
2301B LEU* 3.2 10.6 + - - +
2302B ASN* 2.9 33.2 + - - +
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Residues in contact with ARG2299 (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 PHE* 4.3 0.6 - - - +
2294B GLU* 2.7 43.3 + - + +
2295B SER* 2.9 17.4 + - - +
2296B GLY 3.9 3.8 - - - +
2298B GLY* 1.3 74.3 - - - +
2300B ALA* 1.3 64.9 + - - +
2302B ASN* 3.2 10.9 + - - +
2303B LEU* 3.0 26.8 + - + +
2317B ILE* 4.4 11.8 - - + +
2318B SER 2.9 32.5 + - - +
2319B ALA 4.5 0.4 + - - -
2320B THR* 2.9 32.7 + - - +
2323B TYR* 4.1 25.7 - - - -
2324B PHE* 4.5 2.0 - - - -
2333B PHE* 3.6 28.7 - - + -
2340B MET* 4.9 0.2 - - - -
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Residues in contact with ALA2300 (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 GLY 2.9 19.0 + - - +
2297B VAL 3.7 5.4 - - - +
2298B GLY 3.3 0.2 - - - -
2299B ARG* 1.3 77.5 - - - +
2301B LEU* 1.3 62.2 + - - +
2303B LEU* 3.3 3.6 + - - +
2304B GLN* 3.1 27.8 + - - +
2333B PHE* 3.9 12.3 - - + -
2343B PRO* 3.8 6.0 - - + +
2348B ILE* 3.4 18.8 - - + +
2350B VAL* 3.4 26.5 - - + -
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Residues in contact with LEU2301 (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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2106B THR* 3.5 39.0 - - + +
2120B LEU* 3.8 28.0 - - + -
2124B PHE* 4.1 11.4 - - + -
2264B ILE* 3.8 20.4 - - + -
2270B ILE* 3.8 14.4 - - + -
2297B VAL 3.5 8.1 + - - +
2298B GLY* 3.2 12.0 + - - +
2300B ALA* 1.3 77.5 - - - +
2302B ASN* 1.3 68.4 + - - +
2304B GLN* 3.1 8.6 + - - +
2305B PHE* 2.8 21.7 + - - +
2348B ILE* 4.3 10.2 - - + +
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Residues in contact with ASN2302 (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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2264B ILE* 3.9 17.8 + - - +
2265B PRO* 5.1 2.1 - - - +
2289B LEU* 3.5 24.8 - - + +
2290B GLY 4.4 8.6 + - - -
2291B GLY* 4.7 2.4 - - - -
2294B GLU* 3.0 37.5 + - - +
2298B GLY 2.9 17.7 + - - +
2299B ARG* 3.2 10.5 + - - +
2301B LEU* 1.3 76.3 - - - +
2303B LEU* 1.3 54.2 + - - +
2305B PHE* 3.3 2.2 + - - +
2306B ALA* 2.8 37.8 + - - +
2317B ILE* 4.2 16.5 - - + +
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Residues in contact with LEU2303 (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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2131B ILE* 4.0 17.7 - - + +
2133B VAL* 4.9 0.7 - - + -
2299B ARG* 3.0 16.1 + - + +
2300B ALA 3.5 5.8 - - - +
2302B ASN* 1.3 77.1 - - - +
2304B GLN* 1.3 57.2 + - - +
2306B ALA* 3.7 1.1 - - - -
2307B SER* 3.0 30.5 + - - -
2317B ILE* 3.6 28.7 - - + -
2333B PHE* 3.4 36.1 - - + -
2340B MET* 4.0 33.0 - - + -
2341B THR 3.9 8.1 - - - +
2342B VAL* 3.9 8.0 - - - +
2343B PRO* 3.7 19.5 - - + -
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Residues in contact with GLN2304 (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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2119B SER* 3.5 6.9 + - - -
2120B LEU* 3.4 31.2 - - - +
2121B THR* 3.4 22.3 - - + +
2124B PHE* 3.6 15.3 - - + -
2127B THR* 4.3 2.6 - - - +
2300B ALA 3.1 14.9 + - - +
2301B LEU* 3.6 7.3 - - - +
2303B LEU* 1.3 77.4 - - - +
2305B PHE* 1.3 59.6 + - - +
2307B SER* 2.6 22.6 + - - -
2342B VAL* 3.7 10.8 - - + -
2343B PRO* 3.3 24.8 - - + +
2347B GLY 2.9 18.2 - - - +
2348B ILE* 3.5 27.8 - - - +
2349B GLY 4.3 0.2 + - - -
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Residues in contact with PHE2305 (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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2124B PHE* 3.7 26.4 - + + -
2262B LEU* 3.8 11.9 - - + -
2264B ILE* 3.9 20.6 - - + -
2270B ILE* 4.3 6.1 - - + -
2273B ALA* 3.5 35.7 - - + -
2274B LEU* 3.4 31.6 - - + -
2277B ALA* 4.7 2.2 - - + -
2289B LEU* 4.0 17.0 - - + -
2301B LEU 2.8 20.1 + - - +
2302B ASN* 3.8 3.1 - - - +
2304B GLN* 1.3 74.2 - - - +
2306B ALA* 1.3 60.4 + - - +
2307B SER 3.1 1.3 + - - -
2308B GLN* 2.8 40.4 + - - +
2311B PHE* 3.5 28.6 - + - -
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Residues in contact with ALA2306 (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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2128B ARG* 3.2 16.5 + - - -
2131B ILE* 3.9 14.2 - - + +
2289B LEU* 4.1 14.4 - - + -
2302B ASN 2.8 22.4 + - - +
2303B LEU 3.7 0.4 - - - -
2305B PHE* 1.3 71.8 - - - +
2307B SER* 1.3 61.7 + - - +
2308B GLN 3.2 4.6 + - - +
2311B PHE* 3.5 20.3 - - + +
2315B GLY* 6.2 1.6 - - - +
2317B ILE* 3.7 22.2 - - + -
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Residues in contact with SER2307 (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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2121B THR* 4.5 0.2 - - - +
2127B THR* 3.0 19.1 - - - -
2128B ARG* 2.8 52.0 + - - -
2131B ILE* 3.7 10.3 - - - -
2303B LEU 3.0 16.2 + - - -
2304B GLN* 2.6 19.6 + - - -
2306B ALA* 1.3 75.3 - - - +
2308B GLN* 1.3 67.0 + - - +
2309B PRO 3.5 0.7 - - - -
2342B VAL* 3.5 13.8 - - - +
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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