Contacts of the strand formed by residues 360 - 367 (chain A) in PDB entry 4JHN
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 HIS 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE 3.2 14.8 - - - +
19A LYS 3.6 24.2 + - - +
20A SER* 3.8 14.8 - - - +
42A CYS* 3.7 14.7 - - - -
43A GLY 3.2 26.0 - - - -
44A ASP 3.7 9.2 + - - -
45A GLU* 4.1 3.1 - - - -
46A HIS 3.1 18.5 + - - -
47A SER* 2.9 28.2 + - - -
306A HIS* 3.7 5.9 - - - -
326A LYS* 4.0 8.3 - - - +
357A GLY* 2.8 30.1 + - - -
358A GLY 3.7 0.6 - - - -
359A CYS* 1.3 87.4 + - - +
361A MET* 1.3 63.1 + - - +
362A VAL* 4.3 2.5 - - + -
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Residues in contact with MET 361 (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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15A PHE 3.9 0.5 - - - +
16A THR* 3.6 2.8 - - - -
17A PHE* 2.9 45.6 + - + +
20A SER* 5.5 0.2 - - - -
306A HIS* 3.9 5.8 - - - +
308A ALA* 4.2 0.4 - - - -
316A MET* 4.1 9.4 - - + -
318A THR* 4.1 14.6 - - + -
326A LYS 3.4 25.6 - - - +
327A LEU 3.6 21.5 - - - +
328A GLY* 4.0 3.6 - - - +
354A VAL* 3.9 17.3 - - + -
355A ALA 3.3 17.5 - - - +
356A CYS* 3.8 21.3 - - - -
360A HIS* 1.3 77.2 - - - +
362A VAL* 1.3 64.5 + - - +
363A VAL* 4.0 17.3 - - + -
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Residues in contact with VAL 362 (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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14A VAL* 3.3 33.2 - - + -
15A PHE 3.4 4.0 - - - +
16A THR* 4.3 14.4 - - + -
20A SER* 5.3 0.7 - - - -
40A LEU* 3.6 21.2 - - + +
42A CYS* 3.5 24.7 - - - -
47A SER* 3.8 18.2 - - - +
48A ALA 6.1 0.2 - - - +
49A VAL* 5.1 2.5 - - + -
59A PHE* 4.3 7.2 - - + -
354A VAL* 3.3 4.3 - - - +
355A ALA* 2.9 33.0 + - + +
360A HIS* 4.3 4.7 - - + -
361A MET* 1.3 78.1 - - - +
363A VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 363 (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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13A ALA 3.7 0.9 - - - +
14A VAL* 3.2 4.6 - - - -
15A PHE* 2.7 43.0 + - - +
17A PHE* 4.1 12.6 - - + -
40A LEU* 4.0 2.9 - - - -
316A MET* 3.7 23.1 - - + -
346A PHE* 4.0 26.2 - - + -
351A VAL* 3.8 22.4 - - + -
353A LEU 3.5 10.3 - - - +
354A VAL* 4.0 5.2 - - + -
361A MET* 4.0 17.3 - - + -
362A VAL* 1.3 80.5 - - - +
364A PHE* 1.3 66.1 + - - +
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Residues in contact with PHE 364 (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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11A SER 3.2 26.7 - - - -
12A GLY 4.2 1.3 - - - -
13A ALA* 3.3 28.7 - - - -
14A VAL* 4.4 2.2 - - + -
36A VAL* 3.3 19.1 - - + -
37A PRO* 3.7 38.4 - - + -
40A LEU* 3.7 6.5 - - + +
351A VAL* 3.7 1.0 - - - -
352A LYS* 2.8 61.7 + - + -
353A LEU* 2.9 45.9 + - + +
363A VAL* 1.3 72.6 - - - +
365A ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 365 (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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12A GLY* 3.2 1.3 - - - -
13A ALA 3.1 30.6 + - - +
15A PHE* 4.0 4.1 - - + -
346A PHE* 3.9 33.2 - - + -
349A PHE* 3.9 16.5 - - + -
350A ILE 3.3 13.5 - - - +
351A VAL* 4.0 8.7 - - + -
352A LYS* 4.4 0.9 - - - +
363A VAL* 4.1 1.5 + - + -
364A PHE* 1.3 79.7 - - - +
366A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 366 (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 3.9 4.0 - - - +
11A SER* 3.4 25.4 - - - +
12A GLY* 3.8 0.9 - - - -
349A PHE* 3.3 4.9 - - - -
350A ILE* 2.8 37.3 + - + +
352A LYS* 3.8 28.0 - - + +
364A PHE* 5.2 0.2 - - + -
365A ALA* 1.3 72.3 - - - +
367A PRO* 1.3 72.0 - - + +
190C LYS* 6.1 0.7 - - - +
210C GLU* 5.4 2.7 - - - +
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Residues in contact with PRO 367 (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 MET 6.3 0.7 - - - +
9A PRO 4.2 4.9 - - - +
10A ASP* 3.4 24.5 - - - +
12A GLY* 3.9 11.4 - - - -
348A ARG 3.5 9.4 - - - +
349A PHE* 3.5 23.1 - - + -
350A ILE* 6.0 0.9 - - - -
366A ALA* 1.3 86.2 - - - +
368A HIS* 1.3 63.5 + - - +
369A ARG* 3.5 46.0 + - - +
190C LYS* 4.7 8.0 + - - -
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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