Contacts of the strand formed by residues 278 - 285 (chain A) in PDB entry 3Q02
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 PHE 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A MET* 4.3 11.0 - - - -
237A ILE* 5.1 0.4 - - + -
275A LEU* 4.5 5.8 - - + -
276A PRO* 3.3 16.2 - - + -
277A LYS* 1.3 75.3 - - - +
279A SER* 1.3 60.3 + - - +
280A LEU* 4.0 27.6 - - + -
326A ILE* 4.7 7.0 - - + -
327A GLU* 4.0 0.3 - - - -
328A VAL* 3.0 69.8 + - + +
358A PHE* 3.9 27.4 - + - -
360A PHE* 3.9 34.1 - + - -
376A VAL* 4.2 15.0 - - + -
379A PRO* 4.8 8.5 - - + +
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Residues in contact with SER 279 (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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278A PHE* 1.3 74.0 - - - +
280A LEU* 1.3 68.5 + - - +
281A GLU 4.2 0.5 + - - -
325A LYS* 5.1 6.1 + - - +
326A ILE 3.7 3.6 - - - -
327A GLU* 3.3 25.5 + - - +
379A PRO* 5.8 0.6 + - - -
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Residues in contact with LEU 280 (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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31A ASN* 4.0 26.7 - - + +
32A VAL 3.7 22.0 - - - +
33A VAL* 4.0 9.0 - - + +
278A PHE* 4.0 23.8 - - + -
279A SER* 1.3 80.9 + - - +
281A GLU* 1.3 61.0 + - - +
282A THR* 4.8 2.0 - - - +
324A VAL 3.8 0.3 - - - +
325A LYS* 3.3 7.4 - - - +
326A ILE* 2.9 47.3 + - + +
360A PHE* 3.6 33.2 - - + -
375A GLN 4.1 8.3 - - - +
376A VAL* 4.4 5.6 - - + -
378A GLU 5.8 0.4 - - - +
379A PRO* 6.1 1.6 - - + -
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Residues in contact with GLU 281 (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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147A MET 4.3 7.8 - - - +
148A ILE* 4.8 4.0 - - - +
149A SER 4.9 1.9 + - - -
279A SER 4.2 1.6 + - - -
280A LEU* 1.3 76.9 - - - +
282A THR* 1.3 62.4 + - - +
283A GLU 4.4 0.3 + - - -
323A LYS* 3.2 36.1 + - + +
324A VAL 3.3 10.8 - - - +
325A LYS* 4.0 36.4 + - + +
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Residues in contact with THR 282 (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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31A ASN 4.4 6.6 + - - +
32A VAL* 3.7 13.8 - - + -
33A VAL* 2.8 44.1 + - - +
280A LEU* 4.8 1.6 - - - +
281A GLU* 1.3 76.9 + - - +
283A GLU* 1.3 64.4 + - - +
284A VAL* 3.8 24.5 + - + +
322A GLN 3.8 0.9 - - - +
323A LYS* 3.3 5.5 - - - -
324A VAL* 2.9 32.8 + - - +
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Residues in contact with GLU 283 (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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150A ASN 5.2 0.8 - - - +
151A LEU* 2.6 50.6 - - - +
153A GLY 5.0 2.3 + - - -
281A GLU 4.3 0.4 - - - -
282A THR* 1.3 77.1 - - - +
284A VAL* 1.3 71.4 + - - +
285A ASP 4.0 1.5 + - - +
321A LEU* 4.2 21.3 - - + +
322A GLN 3.3 10.3 - - - +
323A LYS* 3.9 20.3 - - + +
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Residues in contact with VAL 284 (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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23A VAL* 3.9 40.4 - - + -
32A VAL* 4.8 1.6 - - + -
33A VAL 4.7 3.6 - - - +
34A PHE* 4.1 18.4 - - + -
282A THR* 3.8 20.4 - - + +
283A GLU* 1.3 79.3 - - - +
285A ASP* 1.3 71.7 + - - +
286A LEU* 3.3 21.2 + - + +
289A PRO* 4.9 0.9 - - + -
321A LEU* 3.6 2.1 - - - -
322A GLN* 2.7 41.8 + - + +
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Residues in contact with ASP 285 (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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283A GLU* 4.0 3.2 + - - +
284A VAL* 1.3 73.7 - - - +
286A LEU* 1.3 58.7 + - - +
287A ARG* 2.9 33.0 + - - +
288A LYS* 4.3 4.6 + - - +
289A PRO* 3.5 14.6 - - - +
319A GLN* 4.4 10.2 - - - +
320A ALA 3.7 5.7 + - - +
321A LEU* 3.9 20.5 - - + +
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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