Contacts of the helix formed by residues 49 - 68 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR 2.7 16.4 + - - -
45D CYS* 3.2 5.2 + - - -
48D VAL* 1.3 77.9 - - - +
50D CYS* 1.3 58.6 + - - -
51D ILE 3.2 0.7 + - - -
52D PRO* 3.3 6.3 - - - +
53D SER* 2.6 36.3 + - - -
172D LEU* 4.6 0.2 - - - +
480D FAD 3.4 21.7 - - - +
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Residues in contact with CYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452C HIS* 4.2 1.8 - - - -
453C PRO* 4.0 13.5 - - + -
45D CYS* 2.1 50.3 + - - -
49D GLY* 1.3 69.8 - - - -
51D ILE* 1.3 60.2 + - + +
53D SER* 2.6 19.4 + - - -
54D LYS* 2.8 24.8 + - - +
328D ALA* 3.9 6.1 - - - -
480D FAD 3.3 53.3 - - + +
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Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C SER* 3.8 29.8 - - - +
396C THR* 3.3 25.9 - - - +
452C HIS* 4.1 13.5 - - - +
453C PRO* 4.1 11.2 - - + -
45D CYS* 3.0 15.4 + - - +
46D LEU* 3.7 23.1 - - + +
50D CYS* 1.3 72.3 - - + +
52D PRO* 1.4 74.2 - - + +
54D LYS* 4.9 1.1 - - - -
55D ALA* 3.1 22.3 + - - +
95D ALA* 4.9 2.9 - - + -
96D VAL* 4.1 18.8 - - + +
99D LEU* 3.9 17.7 - - + -
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Residues in contact with PRO 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D CYS 3.6 3.8 - - - +
46D LEU 3.2 22.2 - - - +
47D ASN 3.7 13.9 - - - +
48D VAL 3.7 3.6 - - - -
49D GLY 3.3 27.8 - - - +
51D ILE* 1.4 82.8 - - + +
53D SER* 1.3 59.6 + - - +
55D ALA* 3.5 2.1 + - + +
56D LEU* 3.2 27.7 + - - +
92D LYS* 3.8 30.3 - - + +
96D VAL* 3.9 10.3 - - + -
172D LEU* 3.8 14.4 - - + -
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Residues in contact with SER 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLY 2.6 18.2 + - - -
50D CYS* 2.6 22.0 + - - -
52D PRO* 1.3 76.2 - - - +
54D LYS* 1.3 85.3 + - - +
55D ALA 3.2 0.2 + - - -
56D LEU* 3.2 3.9 + - - +
57D LEU* 2.8 28.0 + - - +
172D LEU* 3.8 18.5 - - - +
192D GLU* 4.6 6.3 - - - -
193D LEU* 4.9 7.2 - - - -
196D VAL* 4.7 2.0 - - - +
480D FAD 3.7 11.7 - - - -
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ARG* 5.2 7.6 - - + +
396C THR* 3.7 15.0 - - + -
397C ASN* 4.9 2.1 - - - +
453C PRO* 4.1 16.4 - - + -
50D CYS 2.8 23.6 + - - +
53D SER* 1.3 88.8 + - - +
55D ALA* 1.3 58.3 + - - +
57D LEU* 3.5 19.8 - - - +
58D ASN* 2.9 30.8 + - - +
192D GLU* 2.8 21.8 + - - -
359D TYR* 3.4 50.0 - - + -
480D FAD 2.8 26.5 + - - +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C THR* 3.2 22.9 - - + +
51D ILE 3.1 13.6 + - - +
52D PRO* 3.6 10.1 - - + +
54D LYS* 1.3 75.7 - - - +
56D LEU* 1.3 57.4 + - - +
58D ASN* 3.1 3.1 + - - +
59D ASN* 2.9 36.8 + - - -
91D GLN* 3.8 17.3 - - - +
92D LYS* 4.1 19.7 - - + +
95D ALA* 5.2 3.4 - - + -
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PRO 3.2 13.9 + - - +
53D SER* 3.8 4.3 - - - +
55D ALA* 1.3 78.4 - - - +
57D LEU* 1.3 51.3 + - - +
59D ASN* 4.6 2.5 - - - +
60D SER* 2.7 41.6 + - - -
85D LEU* 6.3 0.2 - - + -
88D MET* 4.4 22.7 - - + +
89D MET* 4.0 22.2 - - + -
92D LYS* 3.9 21.8 - - + -
171D ALA 4.9 2.5 - - - +
172D LEU* 3.5 43.3 - - + +
193D LEU* 5.8 1.1 - - + -
196D VAL* 4.0 25.4 - - + -
197D TRP* 5.2 1.6 - - + +
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D SER* 2.8 16.2 + - - +
54D LYS* 3.5 36.1 - - + +
56D LEU* 1.3 74.9 - - - +
58D ASN* 1.3 63.2 + - - +
60D SER* 3.5 3.8 - - - -
61D HIS* 3.0 9.7 + - - +
192D GLU* 3.8 38.6 - - + +
195D SER* 5.1 0.2 - - - -
196D VAL* 3.8 11.9 - - + +
199D ARG* 2.8 35.3 + - - +
359D TYR* 3.4 38.1 - - + +
360D THR* 4.1 8.5 - - + -
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Residues in contact with ASN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ARG* 3.9 16.8 + - - -
396C THR 5.4 0.4 - - - +
397C ASN* 3.5 37.0 + - - +
54D LYS 2.9 17.2 + - - +
55D ALA* 3.6 5.4 - - - +
57D LEU* 1.3 77.6 - - - +
59D ASN* 1.3 65.7 + - - +
61D HIS* 3.2 8.6 + - - +
62D TYR* 3.1 58.9 + - - -
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Residues in contact with ASN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ARG* 2.7 48.5 + - + +
76C ILE* 3.8 3.5 - - - +
55D ALA 2.9 19.8 + - - +
56D LEU* 4.0 3.8 - - - +
58D ASN* 1.3 78.3 - - - +
60D SER* 1.3 58.5 + - - +
62D TYR* 3.1 7.1 + - - +
63D TYR* 2.9 28.1 + - - +
88D MET* 3.6 44.3 + - + +
91D GLN* 2.9 26.2 + - - +
92D LYS 4.7 0.4 - - - +
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU 2.7 28.0 + - - -
57D LEU* 3.0 11.3 + - - -
59D ASN* 1.3 72.9 - - - +
61D HIS* 1.3 58.3 + - - +
63D TYR* 3.3 3.7 + - - +
64D HIS* 2.9 26.7 + - - +
88D MET* 4.1 1.9 - - - -
196D VAL* 3.7 28.9 - - - -
199D ARG* 3.1 20.8 + - - +
200D LEU* 3.9 24.0 - - - -
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Residues in contact with HIS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C TYR* 5.8 1.8 - - - -
57D LEU 3.0 18.6 + - - +
58D ASN* 3.6 7.5 + - - +
59D ASN 3.2 0.4 - - - -
60D SER* 1.3 76.7 + - - +
62D TYR* 1.3 79.8 + + - +
64D HIS* 3.1 10.7 + - - +
65D MET* 3.0 67.7 + - + +
199D ARG* 3.3 17.7 - - - +
361D HIS* 3.3 57.1 + + + -
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Residues in contact with TYR 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C HIS* 5.6 3.2 - + - -
62C TYR* 3.7 39.2 + + - -
65C MET* 6.5 0.7 - - + -
70C ASP* 5.8 0.9 - - - -
71C PHE* 3.6 34.0 - + + -
74C ARG* 4.9 11.7 - - - -
76C ILE* 3.6 12.3 - - + -
58D ASN* 3.1 50.8 + - - -
59D ASN* 3.7 4.3 - - - +
61D HIS* 1.3 88.2 - + - +
63D TYR* 1.3 66.2 + - - +
65D MET* 3.2 11.9 + - + +
66D ALA* 3.1 24.8 + - - +
71D PHE* 5.2 1.1 - + - -
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Residues in contact with TYR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ILE* 3.3 23.2 - - + +
59D ASN 2.9 13.2 + - - +
60D SER* 3.4 10.1 - - - +
62D TYR* 1.3 75.8 - - - +
64D HIS* 1.3 60.1 + - - +
66D ALA* 3.2 0.9 + - - +
67D HIS* 2.9 67.4 + + + +
81D VAL* 3.9 24.6 + - + -
82D ARG* 4.2 0.6 - - - -
83D LEU* 3.8 42.5 + - + +
88D MET* 4.1 5.2 - - + -
199D ARG 3.6 20.4 - - - -
200D LEU* 3.5 31.1 + - + -
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Residues in contact with HIS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D SER 2.9 13.6 + - - +
61D HIS* 3.2 17.5 - - - +
63D TYR* 1.3 82.9 - - - +
65D MET* 1.3 77.0 + - + +
67D HIS* 4.9 2.0 - - - -
68D GLY* 2.8 28.1 + - - +
199D ARG* 4.6 24.6 + - + +
233D GLN* 5.2 15.6 + - + -
2012D SO4 3.0 38.0 + - - -
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Residues in contact with MET 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C TYR* 6.6 0.2 - - + -
61D HIS* 3.0 43.9 + - + +
62D TYR* 3.2 13.4 + - + +
64D HIS* 1.3 114.7 - - + +
66D ALA* 1.3 60.9 + - - +
68D GLY 3.9 1.4 - - - +
70D ASP* 3.6 35.9 + - + +
71D PHE* 3.0 49.4 + - + +
361D HIS* 5.7 2.7 - - + -
2012D SO4 5.0 3.8 - - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 3.7 18.8 - - + -
76C ILE* 4.0 14.1 - - + -
62D TYR 3.1 15.0 + - - +
63D TYR 3.9 2.2 - - - +
65D MET* 1.3 76.9 - - - +
67D HIS* 1.3 64.9 + - - +
68D GLY 3.5 6.1 - - - +
71D PHE* 4.2 7.5 - - + +
78D MET* 3.4 29.7 - - + +
81D VAL* 3.5 14.2 - - + +
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Residues in contact with HIS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D TYR* 2.9 45.3 + + + +
64D HIS* 4.5 2.6 - - - +
66D ALA* 1.3 73.9 - - - +
68D GLY* 1.3 68.9 + - - +
81D VAL* 3.3 44.6 - - + +
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D HIS* 2.8 22.3 + - - -
65D MET 3.9 2.3 - - - +
66D ALA 3.5 8.5 - - - +
67D HIS* 1.3 86.9 + - - +
69D THR* 1.3 65.2 + - - -
70D ASP 3.5 2.4 + - - -
71D PHE 4.8 0.5 + - - -
72D ALA* 5.0 4.9 + - - +
2012D SO4 3.4 15.5 - - - -
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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) + - + + + + + -
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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