Contacts of the strand formed by residues 314 - 324 (chain E) in PDB entry 3HN3
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 GLY 314 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310E GLN* 4.8 0.7 - - - -
311E THR* 2.5 44.3 + - - +
312E SER 3.4 1.4 + - - -
313E LEU* 1.3 79.1 - - - +
315E PRO* 1.3 76.9 - - - +
316E VAL* 4.1 1.0 - - - +
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Residues in contact with PRO 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ARG* 6.1 0.3 - - - -
308E THR* 5.5 4.9 - - + -
309E ALA 3.1 8.7 - - - +
310E GLN* 3.4 21.7 - - + +
313E LEU 5.2 0.3 - - - +
314E GLY* 1.3 86.6 - - - +
316E VAL* 1.3 66.4 + - - +
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Residues in contact with VAL 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ARG* 5.5 17.3 - - + +
224E PRO* 4.0 28.5 - - + -
225E THR* 5.4 3.4 - - - +
226E THR 4.1 7.9 - - - +
307E LEU* 3.8 0.8 - - + +
308E THR* 3.5 6.7 - - - +
309E ALA* 2.9 41.3 + - + -
311E THR* 3.6 27.8 - - + +
313E LEU 5.8 0.9 - - - +
314E GLY 4.1 6.7 - - - +
315E PRO* 1.3 82.3 - - - +
317E SER* 1.3 63.1 + - - +
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Residues in contact with SER 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E SER* 3.3 11.2 - - - -
224E PRO* 3.3 18.2 - - - +
306E GLN* 4.9 5.8 + - - -
307E LEU 3.2 8.5 + - - -
308E THR* 4.6 9.2 + - - +
316E VAL* 1.3 75.5 + - - +
318E ASP* 1.3 60.4 + - - +
319E PHE* 4.2 20.0 - - - -
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Residues in contact with ASP 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E SER* 2.7 23.3 + - - -
36E ARG* 2.8 28.3 + - - -
224E PRO* 3.4 20.5 - - + +
226E THR 4.4 1.3 - - - +
227E TYR* 3.3 2.9 - - - -
228E ILE* 2.8 34.2 + - - +
305E VAL 3.6 0.9 - - - +
306E GLN* 3.4 4.7 - - - -
307E LEU* 2.8 53.5 + - + +
317E SER* 1.3 76.4 - - - +
319E PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLN* 4.5 0.2 - - - +
33E SER* 2.9 34.8 + - - +
34E PRO* 3.9 36.8 - - + -
35E SER* 2.9 13.2 + - - -
36E ARG* 4.0 8.3 + - - -
228E ILE* 4.2 1.1 - - - -
261E ARG* 4.3 6.7 - - - -
304E GLU* 4.4 18.4 - - + -
305E VAL 3.3 5.8 - - - -
306E GLN* 3.3 50.9 - - + -
317E SER* 4.2 16.4 - - - -
318E ASP* 1.3 80.1 + - - +
320E TYR* 1.3 61.5 + - - +
321E THR* 5.8 2.0 - - - +
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Residues in contact with TYR 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 3.8 24.1 - - + +
29E TYR* 2.7 42.8 + - - +
30E PRO* 5.0 0.2 - - + -
31E GLN* 3.4 29.5 + - + -
33E SER* 5.3 0.2 - - - -
36E ARG* 3.7 25.8 - - - -
228E ILE* 3.7 23.2 - - + +
231E ILE* 3.6 22.4 - - + -
303E LEU 3.6 1.6 - - - +
304E GLU* 5.6 0.4 - - - -
305E VAL* 2.8 35.4 + - - +
319E PHE* 1.3 74.4 - - - +
321E THR* 1.3 77.3 + - - +
322E LEU* 4.2 20.1 - - + +
323E PRO* 6.0 0.2 - - + -
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Residues in contact with THR 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLN* 2.7 39.6 + - - -
263E LEU* 5.5 2.0 - - + -
302E SER* 3.6 31.2 - - - +
303E LEU 3.3 9.0 - - - +
304E GLU* 3.8 22.2 + - + +
319E PHE* 5.6 2.3 - - - +
320E TYR* 1.3 79.2 + - - +
322E LEU* 1.3 63.4 + - - +
323E PRO* 4.0 6.3 - - + +
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Residues in contact with LEU 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 5.2 4.3 - - + -
231E ILE* 3.9 28.7 - - + -
233E VAL* 4.2 13.5 - - + -
302E SER* 4.4 1.6 - - - -
303E LEU* 2.8 40.4 + - + +
320E TYR* 4.2 22.2 - - + +
321E THR* 1.3 74.6 - - - +
323E PRO* 1.4 87.2 - - + +
324E VAL* 3.5 4.7 + - + +
439E ASN* 3.6 42.2 - - + +
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Residues in contact with PRO 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLN* 5.6 0.9 - - - +
300E LEU* 4.3 22.2 - - + -
301E TYR 3.5 9.4 - - - +
302E SER* 4.4 4.2 - - - -
321E THR* 4.0 8.3 - - + +
322E LEU* 1.4 101.8 - - + +
324E VAL* 1.3 61.5 + - - +
394E GLN* 5.3 11.0 - - - +
397E ASP* 5.4 7.0 - - + +
439E ASN 4.3 10.9 - - - +
441E PRO* 5.0 2.5 - - + +
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E VAL* 4.3 22.0 - - + -
235E THR* 3.9 27.6 - - + -
244E VAL* 4.4 9.9 - - + -
262E LEU* 4.4 11.9 - - + -
300E LEU* 3.5 5.5 - - - +
301E TYR* 2.7 45.9 + - + +
303E LEU* 3.9 21.1 - - + +
322E LEU* 3.6 12.6 - - + +
323E PRO* 1.3 79.2 - - - +
325E GLY* 1.3 63.6 + - - +
326E ILE* 4.2 9.4 - - + -
439E ASN 5.6 0.9 - - - -
441E PRO* 5.3 0.9 - - - -
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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