Contacts of the strand formed by residues 341 - 346 (chain A) in PDB entry 1L2L
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 ARG 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A HIS* 4.1 4.2 + - - -
290A TYR* 3.0 21.2 + - + +
291A SER* 2.8 39.1 + - - +
292A VAL* 2.9 27.3 + - - +
339A VAL* 3.4 2.5 - - - +
340A LYS* 1.3 82.1 - - - +
342A ILE* 1.3 68.1 + - - +
343A HIS* 4.0 23.5 - - - +
352A ALA* 5.8 2.7 - - - +
353A LEU 3.5 3.4 - - - -
354A THR* 3.7 12.0 - - + +
356A GLU* 3.2 16.1 + - - +
361A VAL* 5.9 0.8 + - - +
364A ALA* 5.2 1.0 - - - +
365A LEU* 4.9 5.5 - - - +
446A SER 4.9 0.4 + - - -
449A ALA* 3.7 14.3 + - - +
450A PHE* 3.7 35.2 - - - +
453A GLU* 2.8 26.8 + - - -
454A PHE* 4.1 13.6 - - - -
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Residues in contact with ILE 342 (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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292A VAL* 3.3 16.2 - - + +
294A LEU* 4.5 7.0 - - + -
330A LEU* 3.8 43.5 - - + +
333A LEU* 4.3 11.2 - - + -
334A ILE* 3.4 33.0 - - + -
339A VAL* 3.6 20.4 - - + +
341A ARG* 1.3 82.7 - - - +
343A HIS* 1.3 68.9 + - - +
344A PHE 4.4 1.3 - - - +
352A ALA* 3.0 9.8 - - - +
353A LEU* 2.9 42.1 + - + +
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL 2.9 12.4 + - - +
293A GLY* 3.2 6.5 - - - -
294A LEU* 3.1 23.7 + - - +
341A ARG* 4.0 22.2 - - - +
342A ILE* 1.3 75.0 - - - +
344A PHE* 1.3 66.4 + - - +
345A HIS* 3.8 12.6 + + + -
350A TYR* 3.6 31.4 - + + -
351A LEU 3.6 4.8 + - - -
352A ALA* 4.5 2.0 - - + +
365A LEU* 3.7 21.5 - - + +
368A SER* 3.9 1.8 + - - -
445A ILE* 3.6 15.6 - - - +
446A SER* 3.8 19.3 - - - -
449A ALA* 3.5 26.3 - - + +
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Residues in contact with PHE 344 (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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294A LEU* 3.4 17.7 - - + -
295A ASN 3.5 25.6 - - - -
296A GLU* 3.6 11.9 - - + -
299A LEU* 3.8 18.6 - - + -
321A ALA* 4.2 1.1 - - + -
326A VAL* 3.6 36.6 - - + -
330A LEU* 4.2 19.7 - - + -
342A ILE 3.9 1.2 - - - -
343A HIS* 1.3 76.0 + - - +
345A HIS* 1.3 59.1 + - - +
346A THR* 2.9 28.0 - - - -
349A TYR* 3.7 30.7 - + - -
350A TYR* 3.1 3.8 - - - -
351A LEU* 2.6 48.4 + - + +
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Residues in contact with HIS 345 (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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269A GLU* 3.1 37.5 + - - -
294A LEU 3.0 11.8 + - - -
295A ASN* 3.0 39.2 - - + +
343A HIS* 3.8 20.9 - + + -
344A PHE* 1.3 75.1 - - - +
346A THR* 1.3 62.8 + - - +
349A TYR 4.0 0.7 - - - -
350A TYR* 3.6 26.0 - - + -
442A GLY* 3.5 24.1 + - - -
445A ILE* 4.0 25.0 - - + +
446A SER* 4.3 5.4 - - - -
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Residues in contact with THR 346 (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 ASN* 5.0 0.2 - - - -
296A GLU* 3.0 38.6 - - + +
320A PRO* 5.8 0.4 - - + -
321A ALA* 4.6 12.3 - - + +
344A PHE* 2.9 33.6 - - - -
345A HIS* 1.3 70.8 + - - +
347A TYR* 1.3 94.2 + - + +
348A GLY 3.3 1.7 + - - -
349A TYR* 3.2 23.1 + - - +
350A TYR* 3.9 12.0 - - - -
429A THR* 4.9 0.9 - - - +
445A ILE* 6.6 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