Contacts of the strand formed by residues 307 - 316 (chain O) in PDB entry 3H1I
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 307 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296O TYR* 3.6 38.5 + + - -
299O VAL* 3.6 25.6 - - + -
300O ALA* 3.5 25.6 - - + -
303O THR* 3.4 28.5 - - + -
305O GLN 3.6 2.5 - - - -
306O PRO* 1.3 76.6 - - - +
308O ASP* 1.3 89.5 + - - +
309O ALA* 4.4 2.0 - - + -
327O ILE 3.3 16.6 - - - +
328O SER* 4.4 8.7 - - - -
336O VAL* 4.7 6.5 - - + -
52V ARG* 2.9 52.2 - - - +
55V MET* 3.5 13.6 - - - +
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Residues in contact with ASP 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283O PRO* 4.9 1.0 - - - +
296O TYR* 3.8 13.9 - - - -
307O PHE* 1.3 89.4 - - - +
309O ALA* 1.3 68.3 + - - +
310O SER* 4.1 3.0 + - - -
325O TYR 3.9 0.6 - - - +
326O THR* 3.5 1.0 - - - -
327O ILE* 2.9 35.2 + - + +
336O VAL* 5.4 0.3 - - - +
55V MET* 3.3 21.6 - - + +
56V SER* 3.0 28.6 - - - -
57V GLY 3.5 5.7 + - - -
59V SER* 3.1 37.0 + - - -
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Residues in contact with ALA 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280O GLY 4.7 1.9 - - - +
293O SER* 4.9 0.9 + - - -
295O LEU* 4.5 12.8 - - + +
296O TYR* 4.6 20.8 + - - +
299O VAL* 4.2 24.7 - - + -
307O PHE* 4.2 6.5 - - + -
308O ASP* 1.3 82.6 + - - +
310O SER* 1.3 67.1 + - - +
325O TYR 3.0 12.8 - - - +
326O THR* 3.9 16.8 - - + -
336O VAL* 5.4 0.2 - - + -
340O ALA* 5.4 0.7 - - + -
59V SER* 3.9 0.9 - - - -
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Residues in contact with SER 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280O GLY 3.7 10.9 + - - -
281O ALA* 4.6 1.3 - - - -
282O GLY* 3.9 19.8 + - - -
283O PRO* 5.2 1.6 - - - +
295O LEU* 3.7 7.2 - - - -
308O ASP* 4.1 5.5 + - - -
309O ALA* 1.3 79.9 + - - +
311O ALA* 1.3 61.6 - - - +
324O PHE* 3.1 8.5 - - - +
325O TYR 3.0 31.4 + - - -
57V GLY* 5.2 1.4 + - - -
59V SER* 3.3 23.8 + - - -
60V ALA 4.4 11.7 - - - -
61V ARG* 6.0 0.4 - - - -
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Residues in contact with ALA 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276O GLN* 3.4 50.4 - - + +
279O LEU* 4.1 15.7 - - + -
280O GLY 3.1 12.9 + - - +
281O ALA* 4.8 3.7 - - + +
295O LEU* 4.5 2.0 - - - -
310O SER* 1.3 76.2 - - - +
312O PHE* 1.3 63.4 + - - +
322O PHE* 5.4 1.6 - - + -
323O GLY 3.5 5.4 - - - +
324O PHE* 4.4 0.9 - - - +
60V ALA 3.9 2.9 - - - +
61V ARG 3.6 12.8 - - - +
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Residues in contact with PHE 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O LEU* 4.3 16.6 - - + -
163O LEU* 4.0 18.8 - - + -
164O HIS* 4.7 9.2 - + - -
256O ALA* 5.6 0.9 - - + -
258O VAL* 3.5 23.1 - - + -
310O SER 3.5 2.0 + - - -
311O ALA* 1.3 67.0 - - - +
313O ASN* 1.3 66.6 + - - +
314O VAL* 3.1 25.1 - - + -
321O LEU* 4.1 13.7 - - + -
322O PHE* 3.3 6.7 - - - -
323O GLY 2.3 55.6 + - - +
324O PHE* 4.0 11.4 - - - +
325O TYR* 5.3 0.9 - + + -
60V ALA* 3.4 33.4 - - + -
61V ARG 4.3 0.2 - - - -
62V ARG* 2.7 31.2 - - - -
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Residues in contact with ASN 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262O ALA* 5.3 2.4 + - - +
269O ALA 5.8 0.2 + - - -
272O PHE* 4.1 9.8 - - - +
273O SER* 3.9 17.6 + - - +
276O GLN* 3.4 25.5 + - - +
311O ALA 3.8 2.0 + - - -
312O PHE* 1.3 82.2 - - - +
314O VAL* 1.3 65.6 + - - +
315O ASN* 3.8 27.7 + - - +
321O LEU 3.4 12.1 - - - +
322O PHE* 3.4 20.5 - - + +
61V ARG 4.1 2.6 + - - -
62V ARG* 3.4 33.3 + - - +
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Residues in contact with VAL 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O HIS* 5.0 2.2 - - + -
262O ALA 3.8 1.4 - - - +
312O PHE* 3.1 41.5 - - + -
313O ASN* 1.3 76.6 + - - +
315O ASN* 1.3 73.4 + - - +
316O TYR* 3.3 42.2 - - + +
320O GLY* 3.1 4.9 - - - -
321O LEU* 2.9 39.7 + - + +
62V ARG* 5.9 0.2 - - - +
63V ASP* 3.5 27.6 - - + +
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Residues in contact with ASN 315 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O GLU* 4.4 1.7 - - - +
262O ALA* 3.1 22.4 - - - +
263O ALA 4.3 3.6 - - - +
264O VAL* 3.2 28.7 - - + +
269O ALA* 4.3 16.5 - - - +
273O SER* 4.9 4.4 + - - -
313O ASN* 3.8 19.5 + - - +
314O VAL* 1.3 80.8 - - - +
316O TYR* 1.3 67.3 + - - +
62V ARG* 3.7 25.2 - - - +
63V ASP* 5.5 2.9 + - - +
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Residues in contact with TYR 316 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O THR* 5.2 10.2 - - + +
102O ARG* 3.5 18.8 - - + -
103O GLU* 3.5 21.5 - - + +
164O HIS* 2.5 44.1 + + - -
168O TYR* 4.0 10.5 - - - -
172O LEU* 3.3 35.7 - - + -
264O VAL* 3.1 17.7 + - - -
314O VAL* 3.3 27.8 - - + +
315O ASN* 1.3 80.0 - - - +
317O SER* 1.3 66.1 + - - +
318O ASP 3.4 0.9 - - - +
319O SER 2.5 30.1 + - - +
320O GLY* 3.9 4.4 - - - -
321O LEU* 4.9 2.7 - - + -
63V ASP* 3.9 17.6 - - + +
64V LEU 4.6 2.1 + - - -
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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