Contacts of the helix formed by residues 46 - 62 (chain B) in PDB entry 4K9N
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 GLN 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 4.9 0.9 - - - +
44B ALA 3.4 0.4 - - - -
45B LEU* 1.3 78.0 - - - +
47B GLU* 1.3 69.0 + - - +
48B ALA* 2.9 38.3 + - - +
49B CYS* 3.0 24.9 + - - +
50B VAL* 3.1 15.5 + - - +
77B ASN* 3.7 27.8 + - - +
433B TYR 5.4 1.9 - - - +
436B SER* 4.1 15.5 + - - +
46D GLN* 4.4 14.8 + - - +
48D ALA* 4.6 10.5 - - - +
77D ASN 5.3 0.4 + - - -
433D TYR* 3.5 47.0 + - + +
434D SER* 5.4 0.2 + - - -
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 3.2 18.2 - - + +
46B GLN* 1.3 72.2 + - - +
48B ALA* 1.3 66.6 + - - +
50B VAL* 3.6 6.1 - - - +
51B VAL* 3.0 28.8 + - - +
69B LEU* 3.8 20.9 - - + -
70B HIS* 4.8 1.0 - - - +
74B GLY* 3.2 39.0 - - - +
77B ASN* 2.9 28.3 + - + -
78B ALA* 4.0 8.5 - - + -
433D TYR* 3.5 10.1 - - - -
602D TZD 2.7 31.1 + - - +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 2.9 19.0 + - - +
47B GLU* 1.3 75.7 - - - +
49B CYS* 1.3 56.1 + - - +
51B VAL 3.7 0.2 + - - -
52B GLY* 3.0 25.5 + - - -
77B ASN 3.7 16.9 + - - +
78B ALA* 4.3 5.6 - - - +
81B ALA* 4.0 13.7 - - + +
404B GLY 4.8 2.4 - - - +
408B PRO* 4.5 2.8 - - - +
433B TYR 5.4 0.9 - - - +
434B SER* 4.2 15.8 + - - +
46D GLN* 4.6 12.1 - - - +
77D ASN* 4.7 7.9 - - - +
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Residues in contact with CYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 4.0 14.4 - - + -
45B LEU 4.9 0.4 - - - +
46B GLN* 3.0 20.3 + - - +
48B ALA* 1.3 74.7 - - - +
50B VAL* 1.3 59.3 + - - +
53B ILE* 2.8 36.6 + - + +
408B PRO* 3.6 7.6 - - - +
434B SER* 3.7 25.4 - - - -
436B SER* 3.6 23.8 - - - -
437B ALA* 3.7 25.4 - - + -
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.6 30.2 - - + +
22B GLY* 3.6 33.9 - - - +
23B ASN* 3.8 13.7 - - + -
44B ALA* 3.8 15.4 - - + +
46B GLN 3.1 14.3 + - - +
47B GLU* 3.2 9.8 + - - +
49B CYS* 1.3 75.4 - - - +
51B VAL* 1.3 63.8 + - - +
53B ILE* 3.5 4.3 + - - +
54B ALA* 3.1 22.0 + - - +
67B ILE* 4.0 5.6 - - + -
69B LEU* 3.9 15.9 - - + -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU 3.0 8.4 + - - +
50B VAL* 1.3 74.4 - - - +
52B GLY* 1.3 61.4 + - - +
54B ALA* 3.3 6.1 + - - +
55B ASP* 2.8 29.6 + - + +
67B ILE* 4.3 15.7 - - + -
69B LEU* 4.3 14.6 - - + -
78B ALA* 3.6 26.9 - - + -
81B ALA* 3.6 26.2 - - + +
82B LEU* 4.2 16.6 - - + -
92B LEU* 3.9 22.2 - - + +
94B VAL* 5.2 1.3 - - + -
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA 3.0 18.4 + - - -
49B CYS 3.7 1.1 - - - -
51B VAL* 1.3 76.5 - - - +
53B ILE* 1.3 60.2 + - - +
55B ASP* 3.3 7.1 + - - +
56B GLY 3.0 19.8 + - - -
81B ALA* 4.4 4.6 - - - +
404B GLY 5.4 0.7 - - - -
405B PHE* 4.9 7.4 - - - -
408B PRO* 4.0 11.9 - - - -
409B ALA* 3.2 17.3 - - - +
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.7 24.2 - - + -
42B ILE* 4.7 7.9 - - + -
44B ALA* 3.9 13.2 - - + -
49B CYS 2.8 23.5 + - - +
50B VAL* 3.8 4.3 - - - +
52B GLY* 1.3 72.2 - - - +
54B ALA* 1.3 62.5 + - - +
57B TYR* 3.0 19.4 + - - +
408B PRO* 3.3 28.2 - - + +
411B ILE* 4.4 13.5 - - + -
412B GLY* 3.3 20.8 - - - +
415B LEU* 5.3 1.8 - - + -
437B ALA* 4.8 3.6 - - + -
440B THR* 3.9 35.9 - - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.7 27.6 - - + -
50B VAL 3.1 17.7 + - - +
51B VAL 3.7 0.9 - - - +
53B ILE* 1.3 76.4 - - - +
55B ASP* 1.3 57.4 + - - +
57B TYR* 3.3 1.1 + - - +
58B ALA* 2.8 31.4 + - - +
65B ALA* 3.5 9.2 - - + +
67B ILE* 3.6 35.2 - - + -
92B LEU* 4.1 2.5 - - + -
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 2.8 19.9 + - + +
52B GLY* 3.4 8.3 - - - +
53B ILE 3.2 0.2 - - - -
54B ALA* 1.3 74.5 - - - +
56B GLY* 1.3 65.7 + - - +
58B ALA* 3.2 1.7 + - - +
59B GLN* 2.9 35.1 + - - +
81B ALA 4.4 4.0 - - - +
84B ASN 4.6 0.3 - - - -
85B ALA* 3.7 22.2 + - - +
88B SER* 4.3 0.5 + - - -
90B SER* 2.5 32.4 + - - -
92B LEU* 3.9 15.4 - - + +
405B PHE* 3.7 18.7 - - + -
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Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY 3.0 11.5 + - - -
53B ILE 3.8 0.9 - - - -
55B ASP* 1.3 75.7 - - - +
57B TYR* 1.3 62.1 + - - +
59B GLN* 3.9 6.2 - - - +
60B ALA* 2.9 28.1 + - - +
396B TYR* 6.2 0.9 - - - -
405B PHE* 5.4 0.9 - - - -
409B ALA* 3.6 28.8 - - - +
413B VAL* 3.6 16.1 - - - +
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 4.5 4.4 + - - -
19B THR* 4.1 9.9 + - - -
21B PHE* 3.6 28.0 - + + -
40B ARG* 2.9 31.4 + - - -
53B ILE 3.0 13.5 + - - +
54B ALA 3.5 7.9 - - - +
55B ASP 3.2 0.2 - - - -
56B GLY* 1.3 75.9 - - - +
58B ALA* 1.3 52.3 + - - +
61B SER* 2.7 53.5 + - - -
64B PRO 5.3 4.5 - - - -
65B ALA* 4.4 8.7 - - + -
412B GLY* 3.5 22.2 - - - +
415B LEU* 4.0 15.3 - - + -
416B ALA* 3.7 26.9 - - + +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA 2.8 18.2 + - - +
55B ASP 3.2 3.6 + - - +
57B TYR* 1.3 76.7 - - - +
59B GLN* 1.3 59.6 + - - +
61B SER* 3.4 1.5 + - - -
62B ARG* 2.9 29.6 + - - -
63B LYS 3.4 23.0 + - - +
65B ALA* 3.8 15.5 - - + +
90B SER* 5.1 1.1 - - - -
91B PRO* 4.1 17.2 - - + +
92B LEU* 3.9 13.7 - - + -
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP* 2.9 37.4 + - - +
56B GLY* 3.9 4.0 - - - +
58B ALA* 1.3 77.3 - - - +
60B ALA* 1.3 61.8 + - - +
62B ARG* 3.6 8.7 + - - +
88B SER* 3.7 20.4 + - - +
90B SER* 3.4 22.3 + - - +
91B PRO* 5.7 1.8 - - + -
238B PRO* 5.0 1.4 - - - +
239B ARG* 3.1 51.8 + - - +
396B TYR* 3.6 26.1 - - + -
405B PHE* 3.7 23.0 - - - -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLY 2.9 17.7 + - - +
59B GLN* 1.3 79.5 - - - +
61B SER* 1.3 61.3 + - - +
62B ARG* 3.4 16.9 + - - +
371B ILE* 5.8 0.2 - - + -
396B TYR* 3.6 14.1 + - - +
413B VAL* 3.9 23.1 - - + -
416B ALA* 3.8 19.3 - - + -
417B GLU* 4.1 20.8 - - + +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR* 2.7 42.3 + - - -
58B ALA* 3.4 8.0 + - - -
60B ALA* 1.3 73.0 - - - +
62B ARG* 1.3 71.8 + - - +
63B LYS* 3.3 31.1 + - - +
64B PRO 5.3 0.3 + - - -
416B ALA* 4.2 12.3 - - - +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ALA 2.9 11.6 + - - -
59B GLN 3.7 11.0 - - - +
60B ALA* 3.2 12.3 + - - -
61B SER* 1.3 80.0 - - - +
63B LYS* 1.3 64.9 + - - +
91B PRO* 5.5 2.5 - - - -
151B GLN* 5.5 6.5 + - - -
212B ASP* 2.9 44.1 + - - -
213B ALA* 3.1 21.7 + - - +
214B ALA 4.7 0.7 - - - -
215B ASN* 3.7 26.4 + - - +
239B ARG* 3.8 10.0 - - - +
392B PRO* 3.8 10.7 - - - +
393B GLY* 3.7 15.9 - - - +
417B GLU* 5.2 4.8 + - - -
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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