Contacts of the strand formed by residues 326 - 333 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261C THR* 3.6 14.1 - - + -
262C PHE 3.4 2.7 - - - -
263C THR* 3.9 9.2 - - + +
319C ASN* 4.2 1.7 - - - +
320C LEU* 4.7 5.0 + - + +
323C GLU* 3.0 31.7 + - + +
325C ARG* 1.3 75.5 - - - +
327C PHE* 1.3 61.7 + - - +
187D THR* 3.5 25.8 - - - +
188D GLY* 3.7 5.6 - - - -
189D LEU* 3.4 57.3 - - + +
261D THR* 3.5 24.2 - - + -
262D PHE* 3.8 5.6 - - - -
263D THR* 4.1 9.9 - - + -
326D PHE* 3.1 35.2 - + - -
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C LEU 3.5 1.2 - - - +
261C THR* 3.1 6.2 - - - +
262C PHE* 2.7 58.0 + + + -
264C ALA* 4.7 1.6 - - + -
268C THR* 3.5 14.1 - - - -
269C SER* 3.7 12.6 - - - -
270C ILE* 3.4 37.5 - - + -
273C ILE* 3.8 14.4 - - + -
319C ASN* 3.3 13.9 - - + +
320C LEU 5.2 1.8 - - - -
323C GLU* 3.4 33.0 - - + -
324C ARG* 3.4 13.0 - - - -
325C ARG* 3.2 33.2 - - - -
326C PHE* 1.3 78.9 - - - +
328C LYS* 1.3 61.0 + - - +
189D LEU* 3.9 5.8 - - - -
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Residues in contact with LYS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ASP* 3.2 26.8 + - - +
260C LEU 3.2 5.4 - - - +
261C THR* 4.0 12.3 + - - +
270C ILE* 4.0 0.9 - - - +
314C ALA 5.5 0.4 - - - +
315C THR* 3.2 10.3 - - - +
318C ASN* 4.3 18.4 - - + +
319C ASN* 2.7 39.9 + - - +
327C PHE* 1.3 74.2 - - - +
329C ILE* 1.3 64.1 + - - +
330C VAL* 4.3 6.1 - - + -
189D LEU* 3.8 22.3 + - + +
190D MET 4.1 13.0 + - - -
191D THR* 2.7 27.6 + - - -
245D GLY* 4.8 0.9 - - - -
246D MET* 3.7 30.1 - - + +
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Residues in contact with ILE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 3.9 28.5 - - + -
178C LEU* 3.6 19.3 - - + -
258C VAL* 3.5 4.3 - - - +
259C ASP* 3.7 1.6 - - - -
260C LEU* 2.8 41.4 + - + +
262C PHE* 3.4 32.1 - - + -
270C ILE* 4.9 3.4 - - + -
273C ILE* 4.1 22.4 - - + -
277C LEU* 4.2 4.3 - - + -
310C TYR* 4.0 23.1 - - + -
315C THR* 4.1 7.0 - - + -
328C LYS* 1.3 79.4 - - - +
330C VAL* 1.3 68.2 + - - +
331C SER* 5.0 0.6 - - - +
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Residues in contact with VAL 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C VAL* 3.7 22.2 - - + -
258C VAL 3.5 3.4 - - - +
259C ASP* 4.2 9.9 - - - +
310C TYR* 3.4 9.4 - - - -
311C ASP* 2.8 41.7 + - + +
314C ALA* 4.3 14.6 - - + -
315C THR* 3.1 17.3 + - - +
328C LYS* 4.3 5.8 - - + -
329C ILE* 1.3 77.5 - - - +
331C SER* 1.3 63.2 + - - +
332C TRP* 4.6 2.9 - - + +
223D PRO* 5.8 0.2 - - + -
246D MET* 3.7 29.2 - - - -
248D PHE* 4.3 11.7 - - + -
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Residues in contact with SER 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C CYS* 3.8 5.0 - - - -
174C ILE* 4.2 17.5 - - - +
257C VAL* 3.4 4.4 - - - +
258C VAL* 2.7 47.5 + - - +
308C SER* 2.4 30.2 + - - -
309C ILE 3.2 21.0 + - - -
310C TYR* 3.4 5.5 + - - -
311C ASP 4.2 0.2 - - - +
329C ILE* 4.1 1.7 + - - -
330C VAL* 1.3 78.2 - - - +
332C TRP* 1.3 58.5 + - - +
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Residues in contact with TRP 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C CYS* 3.6 1.4 - - - -
255C VAL* 3.9 6.3 - - + -
256C SER 3.5 20.0 - - - -
257C VAL* 3.7 20.6 - - + +
296C LEU 4.2 6.7 - - - -
298C SER* 3.4 29.2 - - - -
301C PHE* 3.3 53.4 - + + -
308C SER* 3.4 4.5 - - - -
309C ILE* 2.7 39.3 + - - +
311C ASP* 2.9 34.2 + - + +
330C VAL* 4.6 2.0 - - + +
331C SER* 1.3 75.9 - - - +
333C TYR* 1.3 71.0 + - - +
212D ARG* 4.7 0.2 - - - +
221D ILE* 3.4 35.0 - - + -
223D PRO* 3.2 30.5 - - + -
248D PHE* 5.0 0.2 - + - -
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Residues in contact with TYR 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C CYS* 3.7 39.5 - - + -
167C THR* 3.0 25.7 + - + +
170C CYS* 3.4 20.9 - - + -
192C THR* 3.0 20.8 + - - -
194C HIS* 3.7 5.1 - + - -
255C VAL* 3.5 4.4 - - - +
256C SER* 2.8 67.5 + - - -
257C VAL* 3.5 10.5 - - - -
258C VAL* 4.0 2.0 - - + -
301C PHE* 5.1 1.5 - - - +
306C ARG 5.1 1.6 - - - +
307C SER 3.6 19.5 - - - +
309C ILE* 4.1 9.2 - - - +
332C TRP* 1.3 80.5 - - - +
334C ASP* 1.3 61.5 + - - +
335C ASN* 2.9 24.5 + - + -
338C GLY* 6.4 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