Contacts of the strand formed by residues 326 - 333 (chain A) in PDB entry 1ML3
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 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A THR* 4.0 9.0 - - + -
262A PHE 3.6 2.0 - - - -
263A THR* 3.6 18.6 - - + +
319A ASN* 4.2 1.4 - - - +
320A LEU* 4.5 6.5 + - + +
323A GLU* 3.0 34.2 + - - +
325A ARG* 1.3 74.0 - - + +
327A PHE* 1.3 62.4 + - - +
187B THR* 3.5 26.2 - - + +
188B GLY* 3.7 6.5 - - - -
189B LEU* 3.4 55.5 - - + +
261B THR* 3.2 21.8 - - + -
262B PHE* 3.8 9.6 - - - -
263B THR* 3.9 15.3 - - + -
326B PHE* 3.3 24.0 - + - -
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Residues in contact with PHE 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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261A THR* 3.3 7.3 - - - +
262A PHE* 2.8 60.4 + + + -
264A ALA* 4.5 0.2 - - + -
268A THR* 3.3 29.4 - - + -
269A SER* 3.9 4.7 - - - -
270A ILE* 3.6 31.0 - - + -
273A ILE* 3.7 16.2 - - + -
319A ASN* 3.5 13.0 - - + +
320A LEU 5.5 0.2 - - - -
323A GLU* 3.3 37.2 - - + -
324A ARG* 3.3 12.3 - - - -
325A ARG* 3.2 31.4 - - - -
326A PHE* 1.3 76.3 - - - +
328A LYS* 1.3 60.8 + - - +
189B LEU* 3.9 4.3 - - - -
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Residues in contact with LYS 328 (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 ASP* 2.5 36.5 + - - +
260A LEU 3.2 5.2 - - - +
261A THR* 3.6 14.0 + - - +
270A ILE* 4.1 1.0 - - - +
314A ALA 5.6 0.9 - - - +
315A THR* 3.5 7.9 - - - +
318A ASN* 4.0 19.7 - - + +
319A ASN* 2.9 27.7 + - - +
327A PHE* 1.3 74.6 - - - +
329A ILE* 1.3 71.3 + - - +
330A VAL* 4.4 5.6 - - + -
189B LEU* 3.8 28.3 - - + +
190B MET 4.5 6.0 + - - -
191B THR* 3.0 22.5 + - - -
245B GLY* 5.3 0.2 - - - -
246B MET* 3.7 30.5 - - + +
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Residues in contact with ILE 329 (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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174A ILE* 4.0 34.3 - - + -
178A LEU* 4.0 7.6 - - + -
258A VAL* 3.3 3.3 - - - +
259A ASP* 3.8 0.2 - - - -
260A LEU* 2.8 40.9 + - + +
262A PHE* 3.4 31.2 - - + -
270A ILE* 5.1 2.2 - - + -
273A ILE* 4.0 24.7 - - + -
277A LEU* 4.0 5.8 - - + -
310A TYR* 3.8 27.6 - - + -
315A THR* 3.9 5.6 - - + -
327A PHE* 5.2 0.2 - - + -
328A LYS* 1.3 82.0 - - - +
330A VAL* 1.3 67.1 + - - +
331A SER* 4.1 0.6 + - - -
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Residues in contact with VAL 330 (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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257A VAL* 3.4 24.0 - - + -
258A VAL 3.1 5.6 - - - +
259A ASP* 4.6 3.1 - - - +
310A TYR* 3.6 6.2 - - - -
311A ASP* 2.9 38.5 + - + +
314A ALA* 4.4 10.3 - - + -
315A THR* 3.3 14.4 + - - +
328A LYS* 4.4 11.2 - - + -
329A ILE* 1.3 76.1 - - - +
331A SER* 1.3 64.8 + - - +
332A TRP* 4.6 3.4 - - - +
223B PRO* 6.0 0.2 - - + -
246B MET* 3.8 31.4 - - + -
248B PHE* 3.9 16.8 - - + -
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Residues in contact with SER 331 (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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170A CYS* 3.6 5.8 - - - -
174A ILE* 4.0 19.3 - - - +
257A VAL* 3.7 3.8 - - - -
258A VAL* 2.6 45.7 + - - +
308A SER* 2.5 29.9 + - - -
309A ILE 3.1 20.7 + - - -
310A TYR* 3.3 2.4 + - - -
311A ASP 4.4 0.2 - - - +
329A ILE* 4.1 2.0 + - - -
330A VAL* 1.3 74.7 - - - +
332A TRP* 1.3 57.6 + - - +
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Residues in contact with TRP 332 (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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170A CYS* 3.8 0.3 - - - -
255A VAL* 3.9 6.3 - - + -
256A SER 3.5 20.9 - - - -
257A VAL* 3.8 22.2 - - + +
296A LEU 4.3 5.8 - - - -
298A SER* 3.5 26.9 - - - -
301A PHE* 3.3 52.6 - + + -
308A SER* 3.5 2.1 - - - -
309A ILE* 2.8 45.5 + - + +
311A ASP* 2.9 31.0 + - + +
330A VAL* 4.6 1.0 - - - +
331A SER* 1.3 77.0 - - - +
333A TYR* 1.3 65.8 + - - +
212B ARG* 4.7 0.2 - - - +
221B ILE* 3.3 37.0 - - + -
223B PRO* 3.3 29.2 - - + -
248B PHE* 4.9 1.8 - + - -
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Residues in contact with TYR 333 (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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166A CYS* 3.6 28.5 - - + -
167A THR* 2.8 31.4 + - - +
170A CYS* 3.3 16.2 - - + -
192A THR* 2.9 17.8 + - - -
194A HIS* 3.3 7.9 - - - -
255A VAL* 3.6 3.3 - - - -
256A SER* 3.0 53.6 + - - -
257A VAL* 3.6 9.6 - - - -
258A VAL* 3.8 16.6 - - + -
301A PHE* 5.3 0.9 - - - -
306A ARG 5.2 0.9 - - - +
307A SER 3.3 20.6 - - - +
309A ILE* 4.0 7.9 - - - -
332A TRP* 1.3 80.4 - - - +
334A ASP* 1.3 61.7 + - - +
335A ASN* 3.0 30.8 + - + -
338A GLY* 6.5 0.2 - - - -
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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