Contacts of the helix formed by residues 46 - 62 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLN* 4.3 14.9 + - - +
48A ALA* 4.7 9.1 - - - +
77A ASN 5.3 0.4 + - - -
432A ASN 4.8 0.2 - - - +
433A TYR* 3.3 45.6 + - + +
434A SER* 5.6 0.2 + - - -
23C ASN* 5.0 0.4 - - - +
44C ALA 3.4 0.8 - - - -
45C LEU* 1.3 77.5 - - - +
47C GLU* 1.3 71.3 + - - +
48C ALA* 2.9 35.4 + - - +
49C CYS* 3.0 24.2 + - - +
50C VAL* 3.1 15.0 + - - +
77C ASN* 3.7 29.6 + - - +
433C TYR 5.4 1.8 - - - +
436C SER* 4.0 16.1 + - - +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A TYR* 3.6 10.8 - - - -
603A TZD 2.7 31.5 + - - +
23C ASN* 3.2 16.9 - - + +
46C GLN* 1.3 71.6 + - - +
48C ALA* 1.3 65.9 + - - +
50C VAL* 3.6 6.4 - - - +
51C VAL* 3.0 28.9 + - - +
69C LEU* 3.8 20.9 - - + -
70C HIS* 5.0 1.0 - - - +
74C GLY* 3.3 37.8 - - - +
77C ASN* 2.9 28.7 + - + -
78C ALA* 3.7 7.6 - - + +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 4.6 11.7 - - - +
77A ASN* 4.7 7.6 - - - +
46C GLN* 2.9 18.0 + - - +
47C GLU* 1.3 76.4 - - - +
49C CYS* 1.3 56.7 + - - +
51C VAL 3.6 0.3 + - - -
52C GLY* 2.9 25.3 + - - -
77C ASN 3.7 16.7 + - - +
78C ALA* 4.3 5.2 - - - +
81C ALA* 4.0 14.8 - - + +
404C GLY 4.8 1.8 - - - +
408C PRO* 4.4 2.9 - - - +
433C TYR 5.5 0.2 - - - +
434C SER* 4.2 15.6 + - - +
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Residues in contact with CYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA* 3.9 13.7 - - + -
45C LEU 5.0 0.2 - - - +
46C GLN* 3.0 20.4 + - - +
48C ALA* 1.3 75.0 - - - +
50C VAL* 1.3 66.3 + - - +
53C ILE* 2.9 29.7 + - + +
408C PRO* 4.0 7.6 - - - -
434C SER* 3.8 25.6 - - - -
436C SER* 3.6 24.0 - - - +
437C ALA* 3.7 27.1 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.5 36.7 - - + +
22C GLY* 3.5 28.0 - - - +
23C ASN* 3.9 13.5 - - + +
44C ALA* 3.7 16.1 - - + +
46C GLN 3.1 15.1 + - - +
47C GLU* 3.3 9.8 + - - +
49C CYS* 1.3 74.8 - - - +
51C VAL* 1.3 58.1 + - - +
53C ILE* 3.4 3.9 + - - +
54C ALA* 3.1 26.0 + - - +
67C ILE* 3.9 16.2 - - + -
69C LEU* 3.9 6.1 - - + -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLU 3.0 16.5 + - - +
50C VAL* 1.3 73.5 - - - +
52C GLY* 1.3 55.8 + - - +
54C ALA* 3.3 5.8 + - - +
55C ASP* 2.8 38.0 + - + +
67C ILE* 4.2 23.8 - - + -
69C LEU* 4.3 6.3 - - + -
78C ALA* 3.6 19.5 - - + -
81C ALA* 3.6 26.7 - - + +
82C LEU* 3.9 24.2 - - + -
92C LEU* 3.9 15.4 - - + +
94C VAL* 5.3 1.6 - - + -
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ALA 2.9 19.2 + - - -
49C CYS 3.4 1.3 + - - -
51C VAL* 1.3 76.7 - - - +
53C ILE* 1.3 60.1 + - - +
55C ASP* 3.3 7.4 + - - +
56C GLY 3.0 19.1 + - - -
81C ALA* 4.4 5.3 - - - +
404C GLY 5.4 0.7 - - - -
405C PHE* 4.9 8.1 - - - -
408C PRO* 4.0 11.9 - - - -
409C ALA* 3.2 17.8 - - - +
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Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 3.6 25.4 - - + -
42C ILE* 4.7 7.0 - - + -
44C ALA* 3.8 23.3 - - + -
49C CYS 2.9 22.5 + - - +
50C VAL* 3.8 3.6 - - - +
52C GLY* 1.3 71.6 - - - +
54C ALA* 1.3 67.1 + - - +
55C ASP 3.2 0.2 + - - -
56C GLY 3.3 0.9 + - - -
57C TYR* 2.9 19.9 + - - +
408C PRO* 3.3 29.1 - - + +
411C ILE* 4.3 10.3 - - + -
412C GLY* 3.3 23.9 - - - +
415C LEU* 5.3 1.8 - - + -
437C ALA* 4.7 6.3 - - + -
440C THR* 3.9 24.7 - - + +
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 3.7 26.9 - - + -
50C VAL 3.1 17.0 + - - +
51C VAL 3.6 1.1 - - - +
53C ILE* 1.3 76.6 - - - +
55C ASP* 1.3 53.9 + - - +
57C TYR* 3.4 2.5 + - - +
58C ALA* 2.8 35.7 + - - +
65C ALA* 3.5 7.1 - - + +
67C ILE* 3.5 35.2 - - + -
92C LEU* 4.0 1.8 - - + -
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Residues in contact with ASP 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 2.8 22.1 + - + +
52C GLY* 3.4 10.0 - - - +
53C ILE 3.1 0.2 - - - -
54C ALA* 1.3 70.4 - - - +
56C GLY* 1.3 65.2 + - - +
58C ALA* 3.2 1.9 + - - +
59C GLN* 2.8 40.9 + - - +
81C ALA 4.5 4.5 - - - +
84C ASN* 4.5 1.0 - - - +
85C ALA* 3.8 21.3 + - - +
88C SER* 4.4 0.5 + - - -
90C SER* 2.7 31.1 + - - -
92C LEU* 3.8 16.4 - - + +
405C PHE* 3.7 18.4 - - + -
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Residues in contact with GLY 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLY 3.0 12.3 + - - -
53C ILE 3.8 0.7 - - - -
55C ASP* 1.3 76.4 - - - +
57C TYR* 1.3 56.8 + - - +
59C GLN* 3.9 5.5 - - - +
60C ALA* 2.9 32.9 + - - +
396C TYR* 6.2 0.7 - - - -
405C PHE* 5.3 1.3 - - - -
409C ALA* 3.6 27.7 - - - +
413C VAL* 3.5 16.3 - - - +
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Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP* 4.9 1.4 + - - -
19C THR* 4.3 7.9 + - - -
21C PHE* 3.5 27.6 - + + -
40C ARG* 3.2 30.7 + - - -
53C ILE 2.9 17.3 + - - +
54C ALA 3.5 4.5 - - - +
56C GLY* 1.3 75.7 - - - +
58C ALA* 1.3 53.6 + - - +
61C SER* 2.7 46.0 + - - -
63C LYS* 3.9 35.5 + - + -
64C PRO 5.3 2.0 - - - -
65C ALA* 4.4 8.7 - - + -
412C GLY* 3.5 23.1 - - - +
415C LEU* 4.0 15.9 - - + -
416C ALA* 3.8 27.1 - - + +
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA 2.8 21.2 + - - +
55C ASP 3.7 3.4 - - - +
57C TYR* 1.3 73.9 - - - +
59C GLN* 1.3 59.5 + - - +
61C SER* 3.8 0.7 - - - -
62C ARG* 2.9 29.8 + - - -
63C LYS 3.4 23.3 + - - +
65C ALA* 3.8 15.7 - - + +
90C SER* 5.0 1.1 - - - -
91C PRO* 4.1 15.6 - - + +
92C LEU* 3.8 13.9 - - + -
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Residues in contact with GLN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASP* 2.8 43.8 + - - +
56C GLY* 3.9 4.2 - - - +
58C ALA* 1.3 73.8 - - - +
60C ALA* 1.3 62.8 + - - +
62C ARG* 3.6 7.8 + - - +
88C SER* 3.6 21.2 + - - +
90C SER* 3.4 21.2 + - - +
91C PRO* 5.7 1.3 - - - -
238C PRO* 4.9 1.9 - - - +
239C ARG* 3.1 58.6 + - - +
396C TYR* 3.7 20.3 - - + -
405C PHE* 3.9 21.2 - - - -
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLY 2.9 17.0 + - - +
59C GLN* 1.3 78.4 - - - +
61C SER* 1.3 62.9 + - - +
62C ARG* 3.5 18.0 + - - -
371C ILE* 5.8 0.7 - - + -
396C TYR* 3.5 16.3 + - - +
413C VAL* 4.1 19.5 - - + +
416C ALA* 3.6 21.1 - - + -
417C GLU* 4.2 19.3 - - + +
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TYR* 2.7 33.2 + - - -
58C ALA* 3.6 4.2 + - - -
60C ALA* 1.3 77.3 - - - +
62C ARG* 1.3 73.3 + - - +
63C LYS* 3.2 38.6 + - - +
416C ALA* 4.4 13.0 - - - -
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ALA 2.9 10.3 + - - -
59C GLN* 3.8 10.1 - - - +
60C ALA 3.2 13.1 + - - -
61C SER* 1.3 80.4 - - - +
63C LYS* 1.3 58.0 + - - +
91C PRO* 5.5 2.9 - - - -
151C GLN* 5.5 5.4 + - - -
212C ASP* 2.9 44.1 + - - -
213C ALA* 3.1 21.3 + - - +
214C ALA 4.6 0.9 - - - -
215C ASN* 3.7 26.9 + - - +
239C ARG* 3.8 9.2 - - - +
392C PRO* 3.8 11.5 - - - +
393C GLY* 3.8 15.5 - - - +
396C TYR* 5.8 0.2 - - - -
417C GLU* 5.4 3.8 + - - -
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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