Contacts of the strand formed by residues 2221 - 2229 (chain A) in PDB entry 5W0P
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 ILE2221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2210A LEU* 4.5 4.3 - - + -
2215A TYR* 3.7 40.2 - - + +
2219A GLU 4.0 6.7 - - - +
2220A PRO* 1.3 75.0 - - - +
2222A PRO* 1.3 66.8 - - - +
2223A VAL* 3.6 15.4 + - + +
2242A VAL* 4.8 6.3 - - + -
2279A LEU 3.6 0.7 - - - +
2280A VAL* 3.4 3.3 - - - +
2281A LEU* 3.0 37.6 + - + +
2283A PRO* 3.6 26.9 - - + -
2330A ILE* 4.4 11.4 - - + -
2354A PHE* 3.6 32.8 - - + -
2356A LEU* 4.9 1.1 - - + -
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Residues in contact with PRO2222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2210A LEU* 3.3 24.1 - - - +
2211A SER* 3.2 28.2 + - - +
2215A TYR* 3.5 10.5 + - + +
2220A PRO* 3.3 13.5 - - + +
2221A ILE* 1.3 83.0 - - - +
2223A VAL* 1.3 60.0 + - - +
2224A THR* 3.9 1.9 + - - +
2278A THR* 4.0 16.6 - - + -
2279A LEU 3.8 4.3 - - - +
2280A VAL* 4.3 12.3 - - + -
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Residues in contact with VAL2223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2208A VAL* 3.9 19.7 - - + -
2210A LEU* 3.8 15.7 - - + -
2221A ILE* 4.0 9.0 - - + +
2222A PRO* 1.3 75.5 - - - +
2224A THR* 1.3 59.7 + - - +
2225A VAL* 3.5 24.4 + - + +
2240A VAL* 3.9 17.3 - - + -
2277A LYS 3.6 0.9 - - - +
2278A THR* 3.4 4.3 - - - +
2279A LEU* 2.9 33.4 + - - +
2281A LEU* 3.6 24.5 - - + -
2330A ILE* 3.8 18.6 - - + -
2332A VAL* 4.0 1.1 - - + -
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Residues in contact with THR2224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2207A SER 3.7 1.2 - - - +
2208A VAL* 3.4 3.1 - - - +
2209A SER* 2.7 59.1 + - - -
2210A LEU 5.6 1.0 - - - -
2222A PRO* 3.9 2.1 + - - +
2223A VAL* 1.3 69.6 - - - +
2225A VAL* 1.3 65.1 + - - +
2226A THR* 4.2 4.3 - - - +
2276A THR* 4.3 19.5 - - + -
2277A LYS 3.8 2.7 - - - +
2278A THR* 3.4 28.2 + - - +
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Residues in contact with VAL2225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2206A LEU* 4.1 13.2 - - + -
2207A SER 3.7 3.4 - - - +
2208A VAL* 4.8 2.0 - - + -
2223A VAL* 3.8 26.2 - - + +
2224A THR* 1.3 79.0 - - - +
2226A THR* 1.3 63.6 + - - +
2227A VAL* 3.9 22.6 + - + +
2238A ILE* 4.9 8.5 - - + -
2240A VAL* 4.6 8.5 - - + -
2275A LEU 3.7 1.7 - - - +
2276A THR* 3.6 2.1 - - - +
2277A LYS* 2.9 38.9 + - + +
2279A LEU* 6.2 1.3 - - + -
2332A VAL* 4.0 33.0 - - + -
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Residues in contact with THR2226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2206A LEU* 3.4 5.2 - - - -
2207A SER* 2.9 44.8 + - - -
2224A THR* 4.8 4.9 - - - +
2225A VAL* 1.3 75.8 + - - +
2227A VAL* 1.3 62.9 + - - +
2228A THR* 3.7 16.3 + - - +
2274A THR* 5.6 4.7 - - - -
2275A LEU 3.6 5.6 - - - +
2276A THR* 3.9 27.8 + - - +
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Residues in contact with VAL2227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2204A LEU* 4.5 18.2 - - + -
2205A ASN 4.0 3.8 - - - +
2206A LEU* 4.0 15.3 - - + +
2225A VAL* 3.9 17.7 - - + +
2226A THR* 1.3 74.5 - - - +
2228A THR* 1.3 62.7 + - - +
2229A ASN 3.9 0.5 + - - -
2235A VAL* 4.6 11.0 - - + -
2238A ILE* 3.8 26.9 - - + -
2269A VAL* 4.5 23.8 - - + +
2273A SER 4.4 0.9 - - - +
2274A THR* 3.4 4.0 - - - -
2275A LEU* 2.9 35.7 + - + +
2334A LEU* 4.3 9.2 - - + -
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Residues in contact with THR2228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2204A LEU* 3.3 5.1 - - - +
2205A ASN* 2.9 52.1 + - + +
2226A THR* 3.7 15.8 + - - +
2227A VAL* 1.3 72.1 - - - +
2229A ASN* 1.3 61.1 + - - +
2230A ASN* 3.5 24.7 + - - +
2274A THR* 3.8 21.9 - - + +
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Residues in contact with ASN2229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2204A LEU* 3.7 9.2 - - + +
2227A VAL* 3.9 1.0 + - + -
2228A THR* 1.3 71.6 - - - +
2230A ASN* 1.3 62.6 + - - +
2231A THR* 2.9 35.5 + - - +
2233A LYS 3.0 21.6 + - - -
2235A VAL* 4.2 11.7 - - - +
2269A VAL* 3.2 30.2 + - + +
2270A GLN 3.5 9.8 + - - +
2271A PRO* 4.0 2.0 - - - -
2272A ASN* 2.9 24.3 + - - -
2273A SER 3.3 24.0 + - - +
2274A THR* 5.7 0.5 - - - +
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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