Contacts of the helix formed by residues 2295 - 2307 (chain B) in PDB entry 1WUF
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 ALA2295 (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* 4.3 3.8 - - + -
2029B LYS* 4.5 0.8 - - + +
2031B PHE* 3.7 33.7 - - + -
2047B GLU* 2.9 24.7 + - - +
2293B LEU 3.7 1.4 + - - -
2294B GLU* 1.3 78.2 - - - +
2296B GLY* 1.3 67.3 + - - +
2297B VAL 3.3 1.5 + - - -
2298B GLY 3.4 0.2 + - - -
2299B ARG* 3.1 17.0 + - - +
2324B PHE* 4.3 7.9 - - + -
2327B ASP* 3.6 14.1 - - - +
2328B ILE* 3.9 6.3 - - + -
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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 ALA* 1.3 77.0 - - - +
2297B VAL* 1.3 55.0 + - - +
2299B ARG* 3.5 5.3 + - - +
2300B ALA* 3.1 28.6 + - - +
2327B ASP* 2.8 28.6 + - - -
2328B ILE* 3.9 2.7 - - - +
2329B VAL* 3.5 28.2 - - - +
2333B PHE* 4.3 5.1 - - - -
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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 ILE* 3.6 23.3 - - + -
2045B TYR* 3.8 41.5 - - + +
2046B GLY 4.0 13.2 - - - -
2047B GLU* 3.6 6.5 + - + +
2295B ALA* 3.4 1.0 - - - +
2296B GLY* 1.3 71.7 - - - +
2298B GLY* 1.3 69.0 + - - +
2300B ALA* 3.3 13.1 + - - +
2301B HIS* 3.3 19.5 + - - +
2328B ILE* 4.4 2.5 - - + -
2329B VAL* 4.4 4.7 - - + -
2348B ILE* 4.2 10.3 - - + -
2352B LEU* 3.8 24.2 - - + -
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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* 2.6 31.6 + - - -
2049B GLU* 4.2 3.8 - - - -
2106B LEU* 6.5 0.7 - - - -
2264B LEU* 5.5 0.3 - - - +
2294B GLU* 3.5 23.7 - - - +
2295B ALA 3.4 0.4 + - - -
2297B VAL* 1.3 74.6 - - - +
2299B ARG* 1.3 61.2 + - - +
2301B HIS* 3.4 6.3 + - - +
2302B ASN* 3.1 22.2 + - - +
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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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2294B GLU* 2.9 36.2 + - - +
2295B ALA 3.1 11.2 + - - +
2296B GLY 3.8 2.9 - - - +
2298B GLY* 1.3 74.7 - - - +
2300B ALA* 1.3 65.9 + - - +
2302B ASN* 3.2 6.8 + - - +
2303B ILE* 2.9 32.2 + - + +
2317B ILE* 3.6 21.5 - - + +
2318B SER* 3.3 34.5 + - - +
2320B SER* 3.8 18.3 + - - +
2323B PHE* 5.6 7.1 - - - -
2324B PHE* 3.9 10.7 - - - -
2327B ASP* 3.4 18.6 + - - -
2333B PHE* 3.5 33.4 - - + -
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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 3.1 17.6 + - - +
2297B VAL 3.3 6.0 + - - +
2299B ARG* 1.3 76.5 - - - +
2301B HIS* 1.3 62.5 + - - +
2303B ILE* 3.5 4.0 + - - +
2304B ALA* 3.4 18.0 + - - +
2333B PHE* 4.2 14.5 - - + -
2343B PRO* 5.1 4.6 - - + +
2348B ILE* 3.6 34.5 - - + +
2350B VAL* 3.8 18.8 - - + -
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Residues in contact with HIS2301 (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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2045B TYR 2.9 28.3 - - - -
2046B GLY* 4.4 1.7 - - - -
2047B GLU 5.5 0.6 + - - -
2106B LEU* 2.9 53.6 + - + +
2109B TRP* 5.3 0.7 - - + -
2110B ASP* 4.0 4.6 + - + +
2120B LEU* 4.5 17.2 - - + +
2264B LEU* 3.9 16.2 - - + +
2270B MET* 5.6 0.9 - - - +
2297B VAL* 3.3 24.4 + - + +
2298B GLY* 3.7 8.4 - - - +
2299B ARG 3.3 0.4 - - - -
2300B ALA* 1.3 74.7 - - - +
2302B ASN* 1.3 67.8 + - - +
2304B ALA* 2.9 18.8 + - - +
2305B LEU* 3.1 12.0 + - - +
2348B ILE* 3.2 28.0 - - + +
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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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2262B LEU 5.4 0.3 - - - +
2263B LYS* 6.0 0.7 - - - -
2264B LEU* 4.2 14.9 + - + +
2289B CYS* 3.5 19.9 - - - +
2290B GLY 3.5 18.3 + - - +
2291B GLY* 4.6 1.6 - - - -
2294B GLU* 3.1 25.7 + - - +
2298B GLY 3.1 12.2 + - - +
2299B ARG* 3.2 12.5 + - - +
2301B HIS* 1.3 79.9 - - - +
2303B ILE* 1.3 56.1 + - - +
2305B LEU* 3.3 9.9 + - - +
2306B ALA* 2.9 26.9 + - - +
2316B ASP 4.7 1.2 + - - -
2317B ILE* 3.7 22.8 - - + +
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Residues in contact with ILE2303 (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* 3.7 16.4 - - + +
2299B ARG* 2.9 22.6 + - + +
2300B ALA 3.9 4.9 - - - +
2301B HIS 3.2 0.2 - - - -
2302B ASN* 1.3 73.4 - - - +
2304B ALA* 1.3 65.1 + - - +
2306B ALA* 3.5 3.4 + - - +
2307B ALA* 3.1 21.5 + - - +
2317B ILE* 3.7 26.9 - - + -
2333B PHE* 3.4 38.8 - - + -
2340B LEU* 3.8 19.7 - - + -
2341B LYS 4.6 3.1 - - - +
2342B VAL* 4.1 14.4 - - + -
2343B PRO* 4.0 20.6 - - + -
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Residues in contact with ALA2304 (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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2120B LEU* 3.2 34.3 - - + -
2121B ALA* 3.8 27.4 - - + +
2124B ILE* 3.0 17.8 - - + +
2126B ALA* 4.2 1.2 - - - +
2300B ALA 3.4 10.4 + - - +
2301B HIS 2.9 6.3 + - - +
2303B ILE* 1.3 75.4 - - - +
2305B LEU* 1.3 66.4 + - - +
2307B ALA* 3.4 13.2 + - - +
2308B ARG 4.0 0.9 + - - -
2342B VAL* 4.9 1.1 - - - -
2343B PRO* 5.6 1.3 - - + +
2348B ILE* 6.3 0.2 - - - -
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Residues in contact with LEU2305 (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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2120B LEU* 5.3 0.4 - - - +
2124B ILE* 3.9 7.6 - - - +
2262B LEU* 4.5 12.8 - - + +
2264B LEU* 3.6 31.9 - - + +
2270B MET* 3.3 30.7 - - + -
2273B ALA* 3.8 15.9 - - + -
2274B LEU* 4.2 7.4 - - + -
2289B CYS* 3.9 17.7 - - + -
2301B HIS 3.1 9.7 + - - +
2302B ASN* 3.5 11.7 - - - +
2304B ALA* 1.3 77.6 - - - +
2306B ALA* 1.3 62.7 + - - +
2308B ARG* 3.0 16.3 + - - +
2311B PHE* 3.2 37.7 - - + -
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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 LYS* 3.2 17.2 + - - -
2131B ILE* 3.5 32.8 - - + +
2289B CYS* 3.6 22.4 - - + -
2302B ASN 2.9 16.9 + - - +
2303B ILE 3.7 0.9 - - - +
2304B ALA 3.3 0.2 - - - -
2305B LEU* 1.3 77.1 - - - +
2307B ALA* 1.3 59.0 + - - +
2308B ARG 3.2 3.0 + - - +
2311B PHE* 3.7 10.1 - - + +
2315B GLY* 6.2 2.0 - - - +
2317B ILE* 3.9 7.6 - - + -
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Residues in contact with ALA2307 (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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2126B ALA* 3.3 27.4 - - + +
2127B THR 4.0 1.7 + - - -
2128B LYS* 2.9 37.5 + - + +
2131B ILE* 3.9 3.6 - - + -
2303B ILE 3.1 12.5 + - - +
2304B ALA* 3.5 9.0 - - - +
2305B LEU 3.1 1.2 + - - -
2306B ALA* 1.3 73.0 - - - +
2308B ARG* 1.3 62.4 + - - +
2309B ASN* 5.0 0.3 - - - +
2342B VAL* 4.1 26.0 - - + -
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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