Contacts of the strand formed by residues 326 - 333 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A THR* 3.5 26.9 - - + +
188A GLY* 3.8 3.1 - - - -
189A LEU* 3.4 46.0 - - + +
261A THR* 3.3 23.3 - - + -
262A PHE* 3.9 3.8 - - - -
263A THR* 3.4 23.8 - - + -
326A PHE* 3.3 23.3 - + - -
261B THR* 3.8 13.9 - - + -
262B PHE 3.4 3.6 - - - -
263B THR* 3.8 13.2 - - + -
319B ASN* 4.3 2.3 - - - +
320B LEU* 4.7 5.2 - - + +
323B GLU* 3.0 32.5 + - - +
325B ARG* 1.3 75.4 - - + +
327B PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 327 (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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189A LEU* 3.7 4.3 - - - -
261B THR* 3.2 7.1 - - - +
262B PHE* 2.8 56.9 + + + +
264B ALA* 4.5 3.4 - - + -
268B THR* 3.8 12.1 - - - -
269B SER* 4.0 13.2 - - - -
270B ILE* 3.6 32.1 - - + -
273B ILE* 3.7 17.3 - - + -
319B ASN* 3.3 13.5 - - + +
320B LEU 5.5 1.1 - - - -
323B GLU* 3.5 28.5 - - + -
324B ARG* 3.4 26.2 - - - -
325B ARG* 3.4 26.0 - - - -
326B PHE* 1.3 77.9 - - - +
328B LYS* 1.3 61.9 + - - +
329B ILE* 5.2 0.2 - - + -
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Residues in contact with LYS 328 (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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189A LEU* 3.4 29.1 - - + +
190A MET 4.4 7.7 + - - +
191A THR* 2.8 27.3 + - - -
245A GLY* 5.7 0.9 - - - -
246A MET* 3.4 31.0 - - + +
259B ASP* 3.0 28.6 + - - +
260B LEU 3.2 6.3 - - - +
261B THR* 3.8 13.4 + - - +
270B ILE* 4.0 1.0 - - - +
314B ALA 5.6 0.4 - - - +
315B THR* 3.2 8.8 - - - +
318B ASN* 4.2 18.8 - - + +
319B ASN* 2.7 37.2 + - - +
327B PHE* 1.3 75.3 - - - +
329B ILE* 1.3 69.7 + - - +
330B VAL* 4.5 3.4 - - + -
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Residues in contact with ILE 329 (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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174B ILE* 4.1 27.4 - - + -
178B LEU* 4.1 13.5 - - + -
258B VAL* 3.7 2.6 - - - +
259B ASP 3.9 0.3 - - - -
260B LEU* 2.7 42.2 + - + +
262B PHE* 3.6 29.6 - - + -
270B ILE* 4.7 3.8 - - + -
273B ILE* 3.6 27.6 - - + -
277B LEU* 4.1 4.5 - - + -
310B TYR* 3.9 26.2 - - + -
315B THR* 3.9 9.0 - - + -
328B LYS* 1.3 80.8 - - - +
330B VAL* 1.3 67.2 + - - +
331B SER* 4.1 0.6 + - - -
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO* 5.7 0.2 - - + -
246A MET* 3.7 30.5 - - + -
248A PHE* 4.1 16.8 - - + -
257B VAL* 3.7 22.2 - - + -
258B VAL 3.5 4.0 - - - +
259B ASP* 4.3 7.2 - - - +
310B TYR* 3.6 6.8 - - - -
311B ASP* 2.8 41.3 + - + +
314B ALA* 4.3 14.1 - - + +
315B THR* 3.1 14.9 + - - +
328B LYS* 4.5 6.1 - - + -
329B ILE* 1.3 76.7 - - - +
331B SER* 1.3 64.7 + - - +
332B TRP* 4.6 2.7 - - + +
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Residues in contact with SER 331 (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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170B CYS* 3.6 8.8 - - - -
174B ILE* 4.0 21.2 - - - +
257B VAL* 3.6 4.3 - - - -
258B VAL* 2.7 42.9 + - - -
308B SER* 2.4 30.2 + - - -
309B ILE 3.3 16.6 + - - -
310B TYR* 3.5 3.1 + - - -
311B ASP 4.4 0.2 - - - +
329B ILE* 4.1 2.2 + - - -
330B VAL* 1.3 77.3 - - - +
332B TRP* 1.3 58.9 + - - +
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Residues in contact with TRP 332 (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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212A ARG* 4.7 0.2 - - - +
221A ILE* 3.3 39.5 - - + -
223A PRO* 3.3 26.9 - - + -
170B CYS* 3.9 0.5 - - - -
255B VAL* 3.9 11.7 - - + -
256B SER 3.5 19.5 - - - -
257B VAL* 3.6 23.6 - - + +
296B LEU 4.2 7.9 - - - -
298B SER* 3.5 29.4 - - - -
301B PHE* 3.4 47.2 - + + -
308B SER* 3.4 3.6 - - - -
309B ILE* 2.8 38.8 + - - +
311B ASP* 2.8 31.8 + - + +
330B VAL* 4.6 1.0 - - - +
331B SER* 1.3 74.5 + - - +
333B TYR* 1.3 67.6 + - - +
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Residues in contact with TYR 333 (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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166B CYS* 3.8 30.3 - - + -
167B THR* 3.1 25.0 + - - +
170B CYS* 3.4 15.9 - - + -
192B THR* 3.2 16.3 + - - -
194B HIS* 3.3 9.2 - - - -
255B VAL* 3.5 4.7 - - - +
256B SER* 2.8 58.0 + - - +
257B VAL* 3.7 5.2 - - - -
258B VAL* 3.9 16.8 - - + -
301B PHE* 5.1 1.8 - - - -
306B ARG 5.1 1.6 - - - +
307B SER 3.5 20.0 - - - +
309B ILE* 4.2 8.7 - - - -
332B TRP* 1.3 79.5 - - - +
334B ASP* 1.3 60.7 + - - +
335B ASN* 3.1 37.9 + - + -
338B GLY* 6.4 0.4 - - - -
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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