Contacts of the strand formed by residues 2273 - 2281 (chain A) in PDB entry 4ZWJ
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 SER2273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2229A ASN* 3.2 21.6 + - - +
2269A VAL* 3.3 14.4 - - - +
2270A GLN* 3.4 28.6 + - - +
2271A PRO 3.2 9.3 + - - -
2272A ASN* 1.3 81.6 + - - +
2274A THR* 1.3 67.0 + - - +
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Residues in contact with THR2274 (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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2227A VAL 3.5 4.5 - - - -
2228A THR* 3.6 35.0 - - + -
2229A ASN 4.7 1.6 - - - +
2230A ASN* 5.7 2.7 - - - +
2269A VAL* 4.9 0.2 - - - -
2272A ASN 5.8 0.4 - - - -
2273A SER* 1.3 81.3 - - - +
2275A LEU* 1.3 68.1 + - - +
2276A THR* 6.1 0.2 - - - -
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Residues in contact with LEU2275 (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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2225A VAL 4.2 0.3 - - - +
2226A THR* 3.6 0.9 - - - -
2227A VAL* 2.9 45.1 + - + +
2228A THR* 5.7 0.3 - - - +
2238A ILE* 4.3 15.5 - - + -
2265A THR* 6.1 0.7 - - + -
2267A GLU* 3.6 33.2 - - + +
2268A LYS 5.5 4.0 - - - +
2269A VAL* 4.0 25.4 - - + -
2274A THR* 1.3 78.9 - - - +
2276A THR* 1.3 72.9 + - - +
2277A LYS* 4.1 11.4 - - + +
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Residues in contact with THR2276 (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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2224A THR* 4.6 13.0 - - + -
2225A VAL 3.7 3.4 - - - +
2226A THR* 3.8 24.6 - - + +
2274A THR* 6.1 0.3 - - - -
2275A LEU* 1.3 82.0 + - - +
2277A LYS* 1.3 63.6 + - - +
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Residues in contact with LYS2277 (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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2224A THR* 3.5 3.8 - - - +
2225A VAL* 2.8 46.4 + - + +
2238A ILE* 6.0 1.8 - - + -
2265A THR* 3.9 19.8 + - + +
2267A GLU* 3.0 34.9 + - - +
2275A LEU* 4.1 14.9 - - + -
2276A THR* 1.3 77.4 - - - +
2278A THR* 1.3 71.1 + - - +
2279A LEU* 4.7 19.6 - - + +
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Residues in contact with THR2278 (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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2222A PRO* 3.8 19.9 - - - +
2223A VAL 3.4 6.1 - - - -
2224A THR* 3.5 27.5 + - + -
2277A LYS* 1.3 83.4 - - + +
2279A LEU* 1.3 64.4 + - - +
2280A VAL* 3.9 6.2 + - - +
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Residues in contact with LEU2279 (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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2221A ILE 3.4 2.3 - - - +
2222A PRO* 4.4 0.2 - - - -
2223A VAL* 2.8 33.3 + - - +
2225A VAL* 5.5 4.9 - - + -
2238A ILE* 4.3 17.0 - - + +
2240A VAL* 3.7 31.4 - - + -
2263A GLU* 4.3 20.0 - - + +
2264A GLU* 4.8 1.8 - - - -
2265A THR* 4.3 27.4 - - + +
2277A LYS* 4.1 21.0 - - + +
2278A THR* 1.3 75.0 - - - +
2280A VAL* 1.3 63.4 + - - +
2281A LEU* 3.5 9.8 - - + +
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Residues in contact with VAL2280 (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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2220A PRO* 3.7 29.8 - - + -
2221A ILE 3.4 9.2 - - - +
2222A PRO* 4.2 17.7 - - + -
2263A GLU* 4.0 14.4 - - - +
2278A THR* 3.9 7.4 + - + +
2279A LEU* 1.3 76.2 - - - +
2281A LEU* 1.3 70.0 + - - +
2282A VAL* 4.6 8.4 - - + +
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Residues in contact with LEU2281 (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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2220A PRO 3.9 0.3 - - - -
2221A ILE* 3.0 31.6 + - + +
2223A VAL* 3.5 32.1 - - + -
2240A VAL* 3.6 41.7 - - + +
2242A VAL* 3.7 31.4 - - + -
2261A ALA* 4.0 4.3 - - + +
2262A SER* 4.0 8.5 - - - -
2263A GLU* 3.7 23.1 - - + +
2279A LEU* 3.5 12.6 - - + +
2280A VAL* 1.3 76.2 - - - +
2282A VAL* 1.3 63.8 + - - +
2283A PRO* 3.5 7.5 - - - +
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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