Contacts of the strand formed by residues 314 - 324 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B GLN* 5.0 0.7 - - - -
311B THR* 2.6 43.7 + - - +
312B SER 3.4 1.8 + - - -
313B LEU* 1.3 78.6 - - - +
315B PRO* 1.3 78.2 - - - +
316B VAL* 3.7 1.7 - - - +
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Residues in contact with PRO 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B THR* 5.4 7.6 - - + -
309B ALA 3.3 10.3 - - - +
310B GLN* 3.6 22.9 - - - +
313B LEU 5.1 0.5 - - - +
314B GLY* 1.3 83.7 - - - +
316B VAL* 1.3 65.4 + - - +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG* 5.4 18.4 - - + +
224B PRO* 4.2 18.8 - - + -
225B THR* 5.4 2.9 - - - +
226B THR* 4.2 16.8 - - - +
307B LEU* 3.8 1.1 - - + +
308B THR* 3.5 5.9 - - - +
309B ALA* 2.9 41.3 + - + +
311B THR* 3.4 29.2 - - + +
313B LEU 5.5 1.1 - - - +
314B GLY 3.7 8.1 - - - +
315B PRO* 1.3 81.3 - - - +
317B SER* 1.3 62.1 + - - +
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 3.3 9.8 - - - -
224B PRO* 3.2 19.4 - - - +
306B GLN* 4.8 5.0 + - - -
307B LEU 3.2 8.8 + - - -
308B THR* 4.6 9.7 + - - +
316B VAL* 1.3 75.6 - - - +
318B ASP* 1.3 59.8 + - - +
319B PHE* 3.7 25.6 - - - -
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Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 2.7 24.1 + - - -
36B ARG* 2.9 29.6 + - - -
224B PRO* 3.4 20.1 - - + +
226B THR 4.3 1.3 - - - +
227B TYR* 3.3 2.5 - - - -
228B ILE* 2.7 35.0 + - - +
305B VAL 3.6 0.7 - - - +
306B GLN* 3.4 4.0 - - - +
307B LEU* 2.7 57.9 + - + +
317B SER* 1.3 75.2 - - - +
319B PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 2.9 32.6 + - - +
34B PRO* 3.7 36.3 - - + -
35B SER* 3.0 16.0 + - - -
36B ARG* 3.7 10.4 + - - -
228B ILE* 4.2 1.8 - - - -
304B GLU* 4.9 15.7 - - + -
305B VAL 3.4 5.8 - - - +
306B GLN* 3.4 50.9 - - + -
317B SER* 3.7 23.1 - - - -
318B ASP* 1.3 75.6 + - - +
320B TYR* 1.3 63.3 + - - +
321B THR* 5.9 1.3 - - - +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 3.6 24.2 - - + +
29B TYR* 2.7 37.0 + - - +
30B PRO* 5.1 0.2 - - + -
31B GLN* 3.4 35.4 + - + -
33B SER* 5.1 0.2 - - - -
36B ARG* 3.6 26.7 - - - -
228B ILE* 3.9 18.1 - - + +
231B ILE* 3.7 23.3 - - + -
303B LEU 3.7 0.9 - - - +
304B GLU* 5.4 0.6 - - - +
305B VAL* 2.9 35.9 + - - +
319B PHE* 1.3 76.0 - - - +
321B THR* 1.3 78.2 + - - +
322B LEU* 4.2 19.6 - - + +
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLN* 2.8 40.7 + - - -
263B LEU* 6.1 1.8 - - + -
302B SER* 3.7 29.2 - - - +
303B LEU 3.3 10.8 - - - +
304B GLU* 4.0 19.0 + - + +
319B PHE* 5.9 1.2 - - - +
320B TYR* 1.3 77.5 + - - +
322B LEU* 1.3 62.5 + - - +
323B PRO* 4.1 5.3 - - + +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 5.0 5.2 - - + -
231B ILE* 3.6 36.1 - - + -
233B VAL* 3.8 18.2 - - + -
302B SER* 4.5 2.0 - - - -
303B LEU* 2.8 44.4 + - + +
320B TYR* 4.2 21.5 - - + +
321B THR* 1.3 74.9 - - - +
323B PRO* 1.4 83.7 - - + +
324B VAL* 5.0 0.9 - - + -
439B ASN* 3.9 32.3 - - + +
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Residues in contact with PRO 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLN* 5.7 0.7 - - - +
300B LEU* 4.5 22.7 - - + -
301B TYR 3.6 9.6 - - - +
302B SER* 4.4 4.3 - - - -
321B THR* 4.1 6.5 - - + +
322B LEU* 1.4 101.5 - - + +
324B VAL* 1.3 62.3 + - - +
325B GLY 4.4 0.2 - - - -
394B GLN* 6.4 2.5 - - + -
397B ASP* 5.3 8.5 - - + +
439B ASN 4.2 11.8 - - - +
441B PRO* 4.9 2.1 - - - +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B VAL* 4.3 20.9 - - + -
235B THR* 4.0 26.2 - - + -
244B VAL* 4.2 12.3 - - + -
262B LEU* 4.3 11.7 - - + -
300B LEU* 3.4 5.8 - - - +
301B TYR* 2.8 43.7 + - + +
303B LEU* 3.9 20.9 - - + +
322B LEU* 3.6 11.7 - - + +
323B PRO* 1.3 79.4 - - - +
325B GLY* 1.3 63.3 + - - +
326B ILE* 4.1 10.3 - - + -
439B ASN 5.5 0.9 - - - -
441B PRO* 5.2 0.7 - - - -
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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