Contacts of the strand formed by residues 278 - 286 (chain A) in PDB entry 3ECP
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 THR 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.9 15.4 - - - +
269A ARG* 3.3 33.1 + - - +
270A ILE 3.3 5.0 + - - -
271A THR* 3.5 24.5 - - + +
276A ASN* 4.2 10.3 - - - +
277A ILE* 1.3 75.6 - - - +
279A LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 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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197A LEU* 4.6 8.3 - - + -
201A LEU* 4.3 23.3 - - + -
207A PHE* 3.8 28.5 - - + -
269A ARG* 3.6 10.3 - - - +
270A ILE* 2.7 58.3 + - + +
272A LEU* 4.2 15.5 - - + -
277A ILE* 4.0 14.4 - - + +
278A THR* 1.3 79.3 + - - +
280A ASN* 1.3 65.6 + - - +
301A LEU* 3.9 22.9 - - + -
302A THR 3.8 6.3 - - - +
303A SER* 5.3 0.7 - - - +
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Residues in contact with ASN 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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268A GLY 3.4 4.7 - - - +
269A ARG* 2.5 48.0 + - - +
270A ILE* 4.2 1.1 - - - -
279A LEU* 1.3 81.3 - - - +
281A ALA* 1.3 63.5 + - - +
301A LEU* 3.7 2.4 - - - -
302A THR* 2.9 31.2 + - - +
303A SER 4.0 7.9 + - - -
304A GLU 3.0 24.0 + - - -
305A PRO* 4.2 4.9 - - - +
306A VAL* 3.4 31.1 - - + +
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Residues in contact with ALA 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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224A LEU* 5.7 1.1 - - + -
228A LEU* 3.8 23.2 - - + +
267A SER* 3.3 4.8 - - - -
268A GLY 3.0 31.6 + - - +
270A ILE* 4.0 16.8 - - + -
280A ASN* 1.3 80.4 - - - +
282A VAL* 1.3 65.9 + - - +
299A LEU* 4.3 1.1 - - + -
300A LEU 3.0 12.8 - - - +
301A LEU* 4.1 13.2 - - + -
302A THR* 4.6 0.7 - - - +
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Residues in contact with VAL 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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228A LEU* 4.4 1.8 - - - -
265A LEU* 3.5 29.6 - - + -
266A ARG 3.3 12.3 - - - +
267A SER* 4.2 1.8 - - - -
281A ALA* 1.3 75.3 - - - +
283A LEU* 1.3 62.6 + - - +
284A ALA 4.2 0.4 - - - -
298A TRP 4.0 0.2 - - - +
299A LEU* 3.6 4.2 - - - +
300A LEU* 2.7 36.9 + - + +
302A THR* 4.7 0.9 - - + -
306A VAL* 3.5 32.5 - - + -
312A ALA* 4.1 13.2 - - + +
315A VAL* 3.9 26.9 - - + -
316A ILE* 4.3 10.1 - - + -
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Residues in contact with LEU 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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225A TYR* 3.9 43.1 - - + +
228A LEU* 3.9 37.2 - - + +
229A LYS* 4.2 9.6 - - + +
264A SER 3.7 1.9 - - - +
265A LEU* 3.6 4.0 - - - -
266A ARG* 2.8 43.7 + - + +
282A VAL* 1.3 73.8 - - - +
284A ALA* 1.3 68.3 + - - +
285A GLU* 4.2 11.4 - - + +
297A LYS* 4.5 7.2 - - + -
298A TRP 3.3 20.4 - - - +
299A LEU* 4.1 9.9 - - + -
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Residues in contact with ALA 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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237A TYR* 3.4 27.8 - - + +
263A LEU* 4.4 8.1 - - + -
264A SER 3.5 6.3 - - - +
265A LEU* 3.7 13.9 - - + +
282A VAL* 4.2 0.8 - - - +
283A LEU* 1.3 74.4 - - - +
285A GLU* 1.3 61.6 + - - +
297A LYS* 3.5 2.8 - - - -
298A TRP* 2.8 43.3 + - + +
316A ILE* 4.1 9.8 - - + +
2C T 4.8 1.3 - - + +
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Residues in contact with GLU 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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225A TYR* 2.5 43.3 + - - -
229A LYS* 3.3 26.7 + - - +
263A LEU* 3.4 5.4 - - - +
264A SER* 2.8 40.4 + - - +
283A LEU* 4.2 11.7 - - + +
284A ALA* 1.3 76.4 - - - +
286A GLU* 1.3 73.6 + - - +
295A PRO* 6.0 2.6 - - + +
296A LEU 3.5 12.1 - - - +
297A LYS* 3.8 15.9 - - + -
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Residues in contact with GLU 286 (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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259A ARG* 3.1 40.6 + - - -
261A ALA* 3.9 13.1 - - + +
262A SER 3.7 9.0 - - - +
263A LEU* 3.4 14.1 - - + +
264A SER* 5.3 0.2 - - - -
285A GLU* 1.3 79.9 - - - +
287A ILE* 1.3 70.8 + - - +
288A ASN 3.8 2.9 + - - +
289A PRO* 3.4 30.4 - - + +
290A PRO* 3.9 0.5 - - - +
295A PRO* 3.5 8.1 - - + +
296A LEU* 2.7 49.4 + - - +
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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