Contacts of the helix formed by residues 336 - 348 (chain A) in PDB entry 5JLH
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 TYR 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A MET* 5.1 5.3 - - + +
17A LYS* 3.5 29.8 - - + +
26A PRO* 4.8 10.8 - - + -
29A VAL* 4.5 8.8 - - + +
333A GLU* 3.1 24.2 + - + +
334A ARG 3.1 0.6 - - - -
335A LYS* 1.4 110.6 + - + +
337A SER* 1.3 64.6 + - - +
338A VAL 3.2 2.2 - - - -
339A TRP* 2.8 17.9 + - + -
340A ILE* 3.0 24.9 + - + -
422F VAL* 3.6 47.8 + - + +
425F ASP 5.4 0.2 + - - -
427F VAL* 3.8 20.9 - - + +
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Residues in contact with SER 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 3.7 26.4 - - - -
143A ALA* 3.3 18.2 - - - +
144A SER* 5.3 2.8 + - - -
298A LEU 5.0 1.1 + - - -
299A SER* 4.3 5.4 - - - -
331A PRO* 4.6 7.6 - - - +
333A GLU 3.6 4.3 + - - -
334A ARG* 2.9 36.0 + - - +
335A LYS 3.3 0.4 - - - -
336A TYR* 1.3 77.2 - - - +
338A VAL* 1.3 64.0 + - - +
340A ILE* 3.2 5.0 + - - +
341A GLY* 2.9 20.1 + - - -
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Residues in contact with VAL 338 (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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10A ASP* 3.2 30.1 - - + +
17A LYS* 5.2 2.9 - - - +
105A THR* 3.4 30.1 - - + +
136A GLN* 3.8 26.2 - - + +
139A LEU* 3.6 16.8 - - + +
140A SER* 4.3 3.6 - - - +
153A ASP* 5.3 0.9 - - - +
299A SER* 4.6 16.4 - - - +
300A GLY* 5.4 4.0 - - - +
335A LYS 4.8 0.9 + - - +
336A TYR 3.2 0.4 - - - -
337A SER* 1.3 77.5 - - - +
339A TRP* 1.3 63.2 + - - +
341A GLY* 3.2 3.5 + - - -
342A GLY 2.9 18.4 + - - -
402A MG 4.3 13.0 - - - -
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Residues in contact with TRP 339 (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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8A VAL* 3.1 39.5 + - + +
10A ASP* 4.3 7.2 + - + -
17A LYS* 3.1 41.0 - - + +
18A ALA 3.5 0.2 - - - -
19A GLY* 3.3 36.4 - - - +
20A PHE 3.5 19.1 - - - -
23A ASP 3.6 18.8 - - - -
24A ASP 4.1 1.8 - - - -
25A ALA* 3.2 14.8 - - - -
26A PRO* 3.2 46.2 - - + -
336A TYR* 2.8 10.0 + - - +
338A VAL* 1.3 81.9 - - - +
340A ILE* 1.3 70.8 + - + +
342A GLY* 3.0 3.3 + - - -
343A SER* 2.9 25.3 + - - -
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.8 21.8 - - - +
26A PRO* 5.4 0.7 - - + -
143A ALA* 3.9 19.1 - - + +
333A GLU* 3.6 34.5 - - + +
336A TYR* 3.0 24.6 + - + +
337A SER* 3.7 8.3 - - - +
339A TRP* 1.3 84.6 - - + +
341A GLY* 1.3 65.3 + - - +
343A SER* 2.5 30.8 + - - +
344A ILE* 2.9 9.7 + - + +
429F LYS* 5.5 8.7 - - - +
666F MET* 5.7 9.4 - - + -
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Residues in contact with GLY 341 (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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139A LEU* 3.1 33.7 - - - +
142A TYR* 4.3 0.2 - - - -
143A ALA* 3.7 3.7 - - - +
337A SER 2.9 10.3 + - - -
338A VAL 3.6 2.7 - - - -
340A ILE* 1.3 77.1 - - - +
342A GLY* 1.3 62.0 + - - +
344A ILE* 2.9 26.6 - - - +
345A LEU* 2.9 13.2 + - - +
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Residues in contact with GLY 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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8A VAL* 3.8 9.6 - - - +
103A LEU* 3.3 32.5 - - - +
139A LEU* 3.6 10.4 - - - +
338A VAL 2.9 11.3 + - - -
339A TRP 3.0 4.2 + - - -
341A GLY* 1.3 76.4 - - - +
343A SER* 1.3 55.6 + - - +
345A LEU* 3.2 1.0 + - - -
346A ALA* 2.9 28.2 + - - +
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.1 3.2 - - - +
21A ALA* 4.1 11.5 - - - +
22A GLY 3.7 10.1 + - - -
23A ASP 3.3 26.6 + - - -
339A TRP* 2.9 24.6 + - - -
340A ILE* 2.5 25.9 + - - +
342A GLY* 1.3 77.5 - - - +
344A ILE* 1.3 60.8 + - - +
346A ALA* 3.4 0.5 + - - -
347A SER* 2.6 35.1 + - - -
666F MET* 5.5 0.2 - - - +
667F PHE* 3.9 7.0 - - - -
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Residues in contact with ILE 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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142A TYR* 3.7 37.7 - - + +
143A ALA* 4.7 2.2 - - - +
340A ILE* 2.9 7.4 + - + +
341A GLY* 2.9 34.3 - - - +
343A SER* 1.3 82.0 + - - +
345A LEU* 1.3 60.8 + - - +
347A SER* 3.2 3.5 + - - -
348A LEU* 2.9 42.2 + - + +
559F TRP* 3.5 38.1 - - + +
560F PHE* 4.7 2.9 - - - +
561F PRO* 5.5 0.4 - - + -
666F MET* 5.3 6.3 - - + -
667F PHE* 3.8 19.7 - - + -
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Residues in contact with LEU 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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103A LEU* 4.6 5.8 - - + -
132A TYR* 5.1 2.5 - - + -
134A ALA* 5.1 7.9 - - + -
138A VAL* 5.8 1.1 - - + -
139A LEU* 4.5 18.2 - - + -
142A TYR* 3.3 54.1 - - + +
341A GLY 2.9 15.7 + - - +
342A GLY* 3.6 6.7 - - - +
344A ILE* 1.3 77.6 - - - +
346A ALA* 1.3 62.6 + - - +
348A LEU* 3.1 16.8 + - + +
351A PHE* 3.2 49.4 - - + +
43C MET 6.2 0.2 - - - -
44C VAL* 4.6 11.9 - - + -
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Residues in contact with ALA 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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6A ALA* 3.8 16.9 - - + +
8A VAL* 4.4 5.6 - - + -
21A ALA* 3.5 27.1 - - + -
103A LEU* 4.9 2.9 - - + +
342A GLY 2.9 13.6 + - - +
345A LEU* 1.3 78.6 - - - +
347A SER* 1.3 60.8 + - - +
348A LEU 3.3 7.1 + - - +
351A PHE* 3.8 10.5 - - + -
352A GLN* 4.3 16.5 + - - +
355A TRP* 4.0 16.8 - - + -
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Residues in contact with SER 347 (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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3A GLU* 5.4 0.5 - - - +
21A ALA* 4.0 1.0 - - - +
22A GLY* 3.2 27.1 + - - -
343A SER 2.6 22.4 + - - -
344A ILE 3.5 6.1 - - - -
345A LEU 3.1 0.4 - - - -
346A ALA* 1.3 78.0 - - - +
348A LEU* 1.3 63.5 + - - +
349A SER* 3.4 3.8 + - - -
352A GLN* 5.4 2.3 + - - -
559F TRP* 3.4 32.1 - - - -
663F ARG* 3.8 17.6 + - - +
667F PHE* 3.5 11.8 - - - -
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Residues in contact with LEU 348 (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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142A TYR* 4.7 7.6 - - + -
344A ILE* 2.9 45.1 + - + +
345A LEU* 3.1 15.1 + - + +
346A ALA 3.5 7.4 - - - +
347A SER* 1.3 78.0 - - - +
349A SER* 1.3 66.4 + - - +
351A PHE* 3.5 16.2 + - + +
352A GLN* 3.6 6.2 - - - +
44C VAL* 3.8 30.1 - - + +
556F GLU* 3.3 37.2 - - + +
559F TRP* 4.0 18.4 - - + -
560F PHE* 4.4 14.4 - - + +
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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