Contacts of the strand formed by residues 275 - 281 (chain A) in PDB entry 4TZ1
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 ASP 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A TYR 3.6 0.5 - - - +
271A LEU* 4.5 2.5 - - - -
272A ASP* 2.5 46.8 + - + +
274A ASP* 1.3 81.6 - - - +
276A TYR* 1.3 68.5 + - - +
277A LYS* 3.0 17.1 + - - +
303A PRO* 6.3 0.9 - - + -
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Residues in contact with TYR 276 (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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62A GLY 5.9 1.3 - - - -
64A LEU* 5.3 14.1 - - + -
70A VAL* 3.6 31.8 - - + +
102A MET* 6.3 0.4 - - + -
104A LYS* 4.9 5.9 - - - -
124A LEU* 4.4 18.0 - - + +
269A LEU* 3.9 36.3 - - + -
270A TYR 3.9 5.2 - - - -
271A LEU* 4.6 16.4 - - + -
274A ASP 4.0 3.4 + - - -
275A ASP* 1.3 72.0 - - - +
277A LYS* 1.3 62.0 + - - +
303A PRO* 4.0 1.6 - - - +
304A LEU* 3.0 47.5 + - + +
305A ASP* 4.7 1.6 - - - +
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Residues in contact with LYS 277 (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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269A LEU* 3.2 11.4 - - - +
270A TYR* 3.0 44.6 + - + +
272A ASP* 3.9 36.7 + - - +
275A ASP* 3.6 17.7 - - + +
276A TYR* 1.3 78.5 - - - +
278A VAL* 1.3 66.3 + - - +
301A SER* 3.5 27.2 + - - +
302A LEU 3.1 12.3 - - - +
303A PRO* 4.0 13.0 - - + -
304A LEU* 4.1 3.6 - - - +
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Residues in contact with VAL 278 (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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267A PRO* 4.0 15.7 - - + -
268A PHE 3.3 13.5 - - - +
269A LEU* 4.1 12.1 - - + -
270A TYR* 3.9 3.4 - - - -
277A LYS* 1.3 79.8 - - - +
279A PHE* 1.3 71.0 + - - +
280A VAL* 3.7 7.6 + - + +
301A SER* 3.1 1.9 - - - -
302A LEU* 2.8 34.9 + - + +
304A LEU* 5.3 2.9 - - + -
307A PHE* 3.5 41.3 - - + -
330A LEU* 5.2 2.2 - - + -
350A VAL* 4.7 2.0 - - + -
352A LEU* 4.1 20.2 - - + -
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Residues in contact with PHE 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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126A LEU* 3.6 21.8 - - + -
180A ARG* 4.8 0.2 - - - -
267A PRO* 3.1 27.2 - - - +
268A PHE* 2.9 37.6 + + + -
270A TYR* 3.6 14.0 - - + -
278A VAL* 1.3 70.8 - - - +
280A VAL* 1.3 57.6 + - - +
281A PRO* 3.3 30.9 - - + +
297A PRO* 3.3 48.9 - - + -
299A GLY* 3.7 27.4 - - - -
300A GLU 3.9 3.8 - - - -
301A SER* 3.3 20.6 - - - -
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Residues in contact with VAL 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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267A PRO* 4.2 7.4 - - + -
278A VAL* 3.9 13.9 - - + +
279A PHE* 1.3 75.6 - - - +
281A PRO* 1.3 70.8 - - - +
282A ALA* 4.6 0.2 - - - -
299A GLY* 3.5 13.5 - - - -
300A GLU* 2.9 25.4 + - + +
302A LEU* 3.9 27.4 - - + -
350A VAL* 4.3 8.1 - - + -
377A LYS* 3.6 42.4 - - + +
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Residues in contact with PRO 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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180A ARG* 5.7 2.5 - - - +
264A ARG* 3.6 19.1 - - - +
265A GLU* 3.4 52.4 - - + +
266A LYS 4.0 4.3 - - - +
267A PRO* 3.9 8.5 - - + -
268A PHE* 4.5 5.4 - - + -
279A PHE* 3.3 39.2 - - + +
280A VAL* 1.3 91.2 - - - +
282A ALA* 1.3 62.7 + - - +
283A LYS 3.8 0.2 + - - -
291A SER* 5.9 1.3 - - - +
297A PRO* 5.4 4.7 - - + -
298A GLU 3.9 1.8 - - - +
377A LYS* 5.4 0.2 - - - -
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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