Contacts of the strand formed by residues 319 - 327 (chain A) in PDB entry 1I7M
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 ASN 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A LEU 3.7 0.2 - - - +
285A PHE* 3.5 3.8 - - - -
286A VAL* 2.6 46.2 + - + +
287A ASN 4.3 8.3 + - - -
288A GLN* 4.7 3.8 - - - +
313A ALA 4.5 0.4 - - - +
314A MSE 2.8 34.3 - - - +
317A ASP 3.7 13.5 + - - -
318A TYR* 1.3 76.5 - - - +
320A PHE* 1.3 61.9 + - - +
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Residues in contact with PHE 320 (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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149A MSE 3.5 25.8 - - + -
157A TRP* 3.4 28.3 - + - -
283A THR* 3.8 15.9 - - - -
284A LEU 3.2 18.4 - - - -
285A PHE* 3.6 37.5 - + + -
311A GLN 4.6 0.9 - - - -
312A SER* 2.9 8.1 - - - -
313A ALA* 2.6 52.1 + - + +
315A PHE* 3.5 24.5 - + + -
319A ASN* 1.3 78.1 - - - +
321A VAL* 1.3 70.1 + - - +
322A PHE* 3.6 17.9 - - + -
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Residues in contact with VAL 321 (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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282A THR* 4.0 1.0 + - - +
283A THR* 3.5 2.8 - - - -
284A LEU* 2.9 64.2 + - + +
299A PRO* 4.4 15.3 - - + -
310A CYS* 4.5 9.6 - - - -
311A GLN 3.3 12.8 - - - +
312A SER* 4.6 6.1 - - - -
320A PHE* 1.3 81.6 - - - +
322A PHE* 1.3 69.2 + - - +
323A THR* 4.2 12.3 - - + -
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Residues in contact with PHE 322 (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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149A MSE 3.6 31.6 - - + -
150A GLY* 3.7 12.8 - - - -
155A ASP 4.0 11.4 - - - -
156A CYS* 4.8 0.9 - - - -
157A TRP* 3.8 28.3 - + + -
281A VAL* 3.5 39.7 - - + -
282A THR 3.3 16.2 - - - -
283A THR* 4.0 7.0 - - + -
309A ASP* 4.2 13.5 - - + -
310A CYS* 3.3 2.1 - - - -
311A GLN* 2.7 45.1 + - + +
320A PHE* 3.6 20.0 - - + -
321A VAL* 1.3 74.7 - - - +
323A THR* 1.3 72.3 + - - +
324A SER* 4.3 1.6 - - - -
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Residues in contact with THR 323 (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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281A VAL* 3.0 8.5 - - - +
282A THR* 2.4 54.9 + - - +
299A PRO* 3.5 25.6 - - + +
300A GLN 5.3 2.0 - - - +
307A ARG* 4.9 2.7 - - - -
309A ASP 3.4 8.1 - - - +
310A CYS* 4.3 14.1 - - + -
321A VAL* 4.2 10.5 - - + -
322A PHE* 1.3 84.9 - - - +
324A SER* 1.3 61.7 + - - +
325A PHE* 2.9 28.1 - - + -
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Residues in contact with SER 324 (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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155A ASP* 4.4 12.3 + - - +
280A PHE 3.6 3.8 + - - -
281A VAL* 3.4 19.5 - - - +
307A ARG* 3.3 5.5 - - - +
308A LEU* 2.6 40.2 + - - +
309A ASP* 3.0 33.5 + - - -
322A PHE* 4.3 4.9 - - - -
323A THR* 1.3 75.3 - - - +
325A PHE* 1.3 61.7 + - - +
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A LYS* 3.4 3.8 - - - +
280A PHE* 2.8 73.6 + + + +
282A THR* 4.4 1.3 - - + -
299A PRO* 3.7 17.5 - - + -
300A GLN 4.0 15.3 - - - -
301A LYS* 4.7 0.2 - - - -
302A ILE* 3.6 32.5 - - + -
305A PHE* 3.9 18.2 - - + -
306A LYS 3.6 3.6 - - - -
307A ARG* 3.7 31.4 - - + -
308A LEU* 4.1 2.0 - - - -
323A THR* 2.9 32.5 - - + -
324A SER* 1.3 77.2 + - - +
326A ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 326 (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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278A GLY 3.7 8.5 - - - +
279A LYS* 4.4 7.4 - - + -
305A PHE* 3.3 10.0 - - - -
306A LYS* 2.7 39.5 + - + +
308A LEU* 3.5 19.3 - - + -
325A PHE* 1.3 77.1 - - - +
327A LYS* 1.3 66.4 + - - +
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Residues in contact with LYS 327 (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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276A LYS* 4.5 12.2 + - - +
277A PRO 2.7 28.1 + - - -
278A GLY* 2.9 33.3 + - - +
304A GLY* 4.0 9.2 - - - +
305A PHE* 3.6 21.1 - - + -
306A LYS* 4.9 2.6 - - - +
326A ALA* 1.3 79.0 - - - +
328A LYS* 1.3 68.5 + - - +
329A GLN* 4.4 26.4 + - + +
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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