Contacts of the strand formed by residues 348 - 357 (chain A) in PDB entry 1Q2L
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 SER 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A VAL* 2.9 46.1 - - - +
295A ARG* 5.4 0.2 + - - -
296A ILE 3.2 17.5 - - - -
297A ASP* 4.2 4.5 - - - -
298A ASN* 3.6 2.2 - - - +
342A PRO 3.0 13.0 - - - +
345A ASN* 2.9 30.2 + - - +
346A GLY 3.3 2.3 + - - -
347A ASN* 1.3 89.3 + - - +
349A GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 349 (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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295A ARG* 3.5 9.4 - - - +
296A ILE* 2.7 31.7 + - - -
341A ASP 3.0 14.8 - - - -
342A PRO* 3.2 8.7 + - - -
344A VAL* 3.6 9.4 - - - -
345A ASN* 4.5 2.0 - - - +
348A SER* 1.3 75.6 + - - +
350A VAL* 1.3 69.7 + - - +
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Residues in contact with VAL 350 (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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293A GLU* 3.5 28.7 - - + -
294A PHE 3.4 4.3 - - - +
295A ARG* 3.7 26.0 - - - +
296A ILE* 3.8 6.1 - - - +
339A ASN* 5.5 2.2 + - - +
340A SER* 3.1 4.7 - - - -
341A ASP* 2.8 38.3 + - + +
344A VAL* 4.4 7.9 - - + -
345A ASN* 4.2 7.0 - - - +
349A GLY* 1.3 80.0 - - - +
351A LEU* 1.3 71.1 + - - +
352A ALA* 4.1 10.3 - - + +
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Residues in contact with LEU 351 (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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293A GLU 3.7 0.3 - - - -
294A PHE* 2.8 38.8 + - + +
296A ILE* 3.9 15.5 - - + -
308A ASP* 3.8 22.9 - - + +
311A ILE* 4.9 6.3 - - + -
312A THR* 3.5 25.6 - - + -
315A ILE* 5.9 1.3 - - + -
338A ALA* 5.4 0.7 - - + -
339A ASN 3.3 16.4 - - - +
340A SER* 3.6 10.5 - - - -
350A VAL* 1.3 74.1 - - - +
352A ALA* 1.3 63.8 + - - +
353A ILE* 6.0 0.7 - - + -
445A ARG* 3.8 19.5 - - + -
449A MET* 3.9 30.7 - - + -
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Residues in contact with ALA 352 (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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291A ARG* 4.1 24.5 - - + +
292A VAL 3.4 7.6 - - - +
293A GLU* 4.4 3.4 - - + -
338A ALA* 3.0 6.5 - - - +
339A ASN* 2.8 51.1 + - - +
350A VAL* 4.1 14.3 - - + +
351A LEU* 1.3 76.0 - - - +
353A ILE* 1.3 64.5 + - - +
354A SER* 4.1 0.9 - - - +
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Residues in contact with ILE 353 (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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290A LEU 3.7 1.6 - - - +
291A ARG* 3.2 4.2 - - - -
292A VAL* 2.8 43.1 + - + +
294A PHE* 4.6 7.2 - - + -
315A ILE* 3.7 38.8 - - + -
323A LEU* 5.7 0.2 - - + -
336A ILE* 3.8 28.0 - - + -
337A SER 3.4 8.7 - - - +
338A ALA* 4.2 2.9 - - + -
351A LEU* 5.9 1.6 - - + -
352A ALA* 1.3 77.5 - - - +
354A SER* 1.3 61.7 + - - +
372A ILE* 3.8 32.6 - - + +
376A LEU* 4.4 8.5 - - + -
449A MET* 4.4 14.8 - - + -
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Residues in contact with SER 354 (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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289A VAL* 4.9 2.2 - - - -
290A LEU 3.6 4.5 - - - -
291A ARG* 2.6 44.1 + - - +
335A GLY 4.2 0.2 - - - +
336A ILE* 3.2 5.7 - - - +
337A SER* 2.7 49.2 + - - -
339A ASN* 4.7 6.1 + - - -
352A ALA* 4.1 3.1 - - - +
353A ILE* 1.3 74.5 + - - +
355A ALA* 1.3 60.9 + - - +
356A SER* 4.4 0.4 + - - -
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Residues in contact with ALA 355 (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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289A VAL* 3.2 8.0 - - - +
290A LEU* 2.8 43.8 + - + +
333A VAL* 3.6 18.6 - - + -
335A GLY 3.6 4.0 - - - -
336A ILE* 4.0 17.3 - - + -
354A SER* 1.3 75.3 - - - +
356A SER* 1.3 61.7 + - - +
357A LEU* 3.5 10.6 + - + +
368A VAL* 4.5 11.9 - - + -
372A ILE* 5.2 2.0 - - + -
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Residues in contact with SER 356 (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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288A LYS 3.7 6.7 - - - -
289A VAL* 4.1 12.3 - - - +
333A VAL* 2.8 16.7 - - - +
334A GLU* 2.8 35.8 + - - -
335A GLY 3.1 11.7 + - - -
354A SER 4.2 0.4 - - - -
355A ALA* 1.3 72.3 - - - +
357A LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 357 (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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288A LYS* 2.8 44.8 + - + +
289A VAL* 3.4 34.8 - - - +
290A LEU* 3.4 9.4 - - + +
332A LEU 3.7 13.2 - - - +
333A VAL* 4.2 8.3 - - + -
334A GLU* 3.8 10.3 - - - +
355A ALA* 4.1 11.2 - - + +
356A SER* 1.3 79.0 - - - +
358A THR* 1.3 69.5 + - - +
361A GLY* 3.9 2.9 - - - +
362A LEU* 3.7 21.8 - - + +
365A ARG* 4.8 9.4 - - + -
368A VAL* 4.0 22.9 - - + -
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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