Contacts of the helix formed by residues 49 - 68 (chain C) in PDB entry 1ZMC
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 GLY 49 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR 2.6 16.7 + - - -
45C CYS* 3.6 1.2 + - - -
48C VAL* 1.3 76.1 - - - +
50C CYS* 1.3 66.4 + - - -
51C ILE 3.4 2.7 - - - -
52C PRO* 3.3 5.9 - - - +
53C SER* 3.0 26.7 + - - -
172C LEU* 4.2 0.3 - - - +
480C FAD 3.4 28.3 - - - -
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Residues in contact with CYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C CYS* 2.1 50.0 + - - -
49C GLY* 1.3 69.9 - - - -
51C ILE* 1.3 60.7 + - + +
53C SER* 3.2 2.2 + - - -
54C LYS* 2.9 37.0 + - - +
328C ALA* 4.0 4.7 - - - -
480C FAD 3.4 56.1 - - + -
452D HIS* 4.2 2.0 - - - -
453D PRO* 4.0 13.0 - - + -
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C CYS* 2.9 18.5 + - - +
46C LEU* 3.7 19.7 - - + +
50C CYS* 1.3 78.9 - - + +
52C PRO* 1.4 70.7 - - + +
54C LYS* 4.9 0.2 - - - -
55C ALA* 3.1 18.4 + - - -
95C ALA* 4.7 2.9 - - + -
96C VAL* 4.2 19.3 - - + +
99C LEU* 3.8 20.4 - - + -
392D SER* 4.0 23.6 - - - +
396D THR* 3.1 37.8 - - + +
452D HIS* 4.2 13.9 - - - +
453D PRO* 4.3 8.5 - - + -
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Residues in contact with PRO 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C CYS 3.7 4.0 - - - +
46C LEU 3.3 15.3 - - - +
47C ASN 3.6 13.5 - - - +
49C GLY 3.3 24.9 - - - +
51C ILE* 1.4 93.8 - - + +
53C SER* 1.3 58.9 + - - +
55C ALA* 3.4 2.6 + - + +
56C LEU* 3.1 27.9 + - - +
92C LYS* 3.8 30.6 - - + +
96C VAL* 4.0 10.5 - - + -
172C LEU* 3.8 17.9 - - + -
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Residues in contact with SER 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY 3.0 24.8 + - - -
50C CYS* 3.2 0.9 + - - -
52C PRO* 1.3 78.3 - - - +
54C LYS* 1.3 86.2 + - - +
55C ALA 3.3 0.2 + - - -
56C LEU* 3.3 3.3 + - - +
57C LEU* 2.8 36.7 + - - +
172C LEU* 3.5 20.6 - - - +
192C GLU* 4.0 5.3 + - - -
193C LEU* 4.6 9.0 - - - -
196C VAL* 4.7 0.7 - - - +
480C FAD 3.8 12.7 - - - -
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C CYS 2.9 24.1 + - - +
51C ILE* 4.0 2.0 - - - +
53C SER* 1.3 97.8 + - - +
55C ALA* 1.3 56.7 + - - +
57C LEU* 3.7 17.0 - - - +
58C ASN* 2.9 30.3 + - - +
192C GLU* 2.9 24.7 + - - -
359C TYR* 3.6 41.5 - - + -
480C FAD 2.8 35.2 + - - +
393D ARG* 4.8 10.5 + - - +
396D THR* 3.9 11.2 - - + -
397D ASN* 4.7 3.0 - - - +
453D PRO* 4.0 18.2 - - + -
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Residues in contact with ALA 55 (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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51C ILE 3.1 8.0 + - - +
52C PRO* 3.6 8.3 - - + +
53C SER 3.2 0.4 - - - -
54C LYS* 1.3 72.9 - - - +
56C LEU* 1.3 59.8 + - - +
58C ASN* 3.1 4.5 + - - +
59C ASN* 2.8 36.2 + - - -
91C GLN* 3.8 17.3 - - - +
92C LYS* 4.0 21.1 - - + +
95C ALA* 5.1 1.1 - - + -
396D THR* 3.2 29.2 - - + +
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Residues in contact with LEU 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 PRO 3.1 12.4 + - - +
53C SER* 3.8 4.0 - - - +
55C ALA* 1.3 79.4 - - - +
57C LEU* 1.3 61.1 + - - +
59C ASN* 4.0 3.0 - - - +
60C SER* 2.7 32.2 + - - -
85C LEU* 6.4 0.7 - - + -
88C MET* 4.5 22.9 - - + +
89C MET* 4.0 24.9 - - + -
92C LYS* 4.0 17.3 - - + -
171C ALA 4.8 2.5 - - - +
172C LEU* 3.6 47.1 - - + +
193C LEU* 5.5 0.7 - - + -
196C VAL* 4.0 24.9 - - + -
197C TRP* 5.0 2.2 - - + +
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Residues in contact with LEU 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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53C SER* 2.8 23.2 + - - +
54C LYS* 3.7 30.7 - - - +
56C LEU* 1.3 77.2 - - - +
58C ASN* 1.3 60.8 + - - +
60C SER* 3.0 16.5 + - - -
61C HIS* 3.0 8.4 + - - +
192C GLU* 3.8 31.0 - - + +
195C SER* 4.9 0.4 - - - -
196C VAL* 3.6 19.7 - - + +
199C ARG* 3.0 24.0 + - - +
359C TYR* 3.5 36.6 - - + +
360C THR* 4.1 8.7 - - + -
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Residues in contact with ASN 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 LYS 2.9 18.6 + - - +
55C ALA* 3.6 5.2 - - - +
57C LEU* 1.3 78.3 - - - +
59C ASN* 1.3 62.3 + - - +
61C HIS* 3.3 7.7 + - - +
62C TYR* 3.3 48.6 + - - -
74D ARG* 3.5 21.7 + - - +
393D ARG* 5.6 4.1 - - - +
396D THR 5.4 0.2 - - - +
397D ASN* 3.3 37.5 + - - +
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Residues in contact with ASN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 2.8 25.7 + - - +
56C LEU* 4.0 3.0 - - - +
58C ASN* 1.3 73.3 - - - +
60C SER* 1.3 59.2 + - - +
62C TYR* 3.4 1.3 + - - -
63C TYR 3.0 22.2 + - - -
88C MET* 3.5 51.5 + - + +
91C GLN* 2.7 26.6 + - - +
74D ARG* 2.7 52.5 + - + +
76D ILE* 3.7 4.7 - - - +
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Residues in contact with SER 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 LEU 2.7 24.0 + - - -
57C LEU* 3.0 2.8 + - - -
59C ASN* 1.3 75.1 - - - +
61C HIS* 1.3 64.8 + - - +
63C TYR* 3.5 8.5 + - - +
64C HIS* 3.1 21.3 + - - +
88C MET* 4.3 1.5 - - - -
196C VAL* 3.9 22.3 - - - -
199C ARG* 2.9 41.6 + - - +
200C LEU* 4.1 16.4 - - - -
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Residues in contact with HIS 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 LEU 3.0 17.5 + - - +
58C ASN* 3.8 9.1 + - - +
59C ASN 3.2 0.4 - - - -
60C SER* 1.3 79.3 + - - +
62C TYR* 1.3 76.7 + + - +
64C HIS* 3.1 11.9 + - - +
65C MET* 3.0 64.4 + - + +
199C ARG* 3.8 16.6 - - - +
361C HIS* 3.3 56.0 + + + +
62D TYR* 5.6 2.7 - + - -
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Residues in contact with TYR 62 (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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58C ASN* 3.3 42.2 + - - -
59C ASN* 3.9 2.7 - - - +
60C SER 3.3 0.2 - - - -
61C HIS* 1.3 95.2 - + - +
63C TYR* 1.3 64.8 + - - +
65C MET* 3.2 8.4 + - + +
66C ALA* 3.0 25.8 + - - +
71C PHE* 5.6 0.2 - + - -
61D HIS* 5.8 1.9 - - - -
62D TYR* 3.7 38.7 + + - -
65D MET* 6.6 0.2 - - + -
70D ASP* 5.4 1.1 - - - -
71D PHE* 3.5 33.6 - + + -
74D ARG* 4.3 19.5 - - - -
76D ILE* 3.5 12.3 - - + -
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Residues in contact with TYR 63 (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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59C ASN 3.0 18.2 + - - +
60C SER* 3.8 4.7 - - - +
61C HIS 3.3 0.2 - - - -
62C TYR* 1.3 75.6 - - - +
64C HIS* 1.3 54.8 + - - +
66C ALA 3.6 0.2 - - - -
67C HIS* 2.7 87.6 + + + +
81C VAL* 4.0 17.2 + - + -
82C ARG 4.8 0.4 - - - -
83C LEU* 3.9 38.6 + - + +
88C MET* 4.0 11.7 - - + -
199C ARG 3.5 26.7 - - - -
200C LEU* 3.8 27.2 + - + -
76D ILE* 3.2 17.8 - - + +
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Residues in contact with HIS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C SER 3.1 12.9 + - - +
61C HIS* 3.1 16.7 + - - +
63C TYR* 1.3 79.8 - - + +
65C MET* 1.3 69.6 + - - +
67C HIS* 4.5 2.9 - - - +
68C GLY* 2.9 24.9 + - - +
199C ARG* 4.6 25.4 + - + +
233C GLN* 5.3 19.6 + - + -
2008C SO4 2.7 40.5 + - - -
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Residues in contact with MET 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C HIS* 3.0 54.6 + - + +
62C TYR* 3.2 11.4 + - + +
64C HIS* 1.3 88.0 - - - +
66C ALA* 1.3 60.2 + - - +
68C GLY 4.2 1.6 - - - +
70C ASP* 3.5 48.9 + - + +
71C PHE* 2.9 42.6 + - + +
74C ARG* 5.4 2.5 - - - +
361C HIS* 4.8 7.0 - - + +
398C ALA 5.8 0.9 - - - +
399C ASP* 5.2 10.3 - - + +
62D TYR* 6.5 0.4 - - + -
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TYR 3.0 16.3 + - - +
63C TYR 3.8 2.0 - - - +
65C MET* 1.3 78.1 - - - +
67C HIS* 1.3 62.2 + - - +
68C GLY 3.8 5.1 - - - +
71C PHE* 4.1 6.3 - - + +
78C MET* 3.5 36.5 - - + +
81C VAL* 3.5 10.4 - - + +
71D PHE* 3.8 18.8 - - + -
76D ILE* 3.9 15.0 - - + -
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Residues in contact with HIS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C TYR* 2.7 63.9 + + + +
64C HIS* 4.6 3.4 - - - +
66C ALA* 1.3 71.0 - - - +
68C GLY* 1.3 68.2 + - - +
81C VAL* 3.5 29.6 + - + -
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Residues in contact with GLY 68 (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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64C HIS* 2.9 24.2 + - - -
65C MET 4.2 1.9 - - - +
66C ALA 3.5 6.6 - - - +
67C HIS* 1.3 87.2 + - - +
69C THR* 1.3 61.4 + - - -
70C ASP 3.5 2.6 + - - -
71C PHE 4.9 0.7 + - - -
72C ALA* 5.1 4.7 + - - +
2008C SO4 3.8 13.9 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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