Contacts of the helix formed by residues 49 - 68 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR 2.8 15.6 + - - -
45A CYS* 3.3 5.2 + - - -
48A VAL* 1.3 77.3 - - - +
50A CYS* 1.3 61.1 + - - -
51A ILE 3.3 0.6 + - - -
52A PRO* 3.4 3.4 - - - +
53A SER* 2.8 34.8 + - - -
172A LEU* 4.3 0.2 - - - +
480A FAD 3.4 26.0 - - - +
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Residues in contact with CYS 50 (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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45A CYS* 2.1 48.5 + - - -
49A GLY* 1.3 71.1 - - - -
51A ILE* 1.3 60.3 + - + +
53A SER* 2.9 2.2 + - - -
54A LYS* 2.8 37.8 + - - +
328A ALA* 3.8 5.8 - - - -
480A FAD 3.4 57.8 - - + +
452B HIS* 4.3 1.3 - - - -
453B PRO* 3.9 12.6 - - + -
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Residues in contact with ILE 51 (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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45A CYS* 2.9 18.0 + - - +
46A LEU* 3.6 32.5 - - + +
50A CYS* 1.3 75.4 - - + +
52A PRO* 1.4 68.6 - - + +
54A LYS* 3.2 0.6 + - - -
55A ALA* 3.1 16.2 + - + +
95A ALA* 5.1 2.7 - - + -
96A VAL* 3.9 20.6 - - + +
99A LEU* 4.0 10.1 - - + -
392B SER* 4.0 24.9 - - - +
396B THR* 3.4 34.4 - - + +
452B HIS* 4.2 9.2 - - - +
453B PRO* 4.1 15.3 - - + -
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Residues in contact with PRO 52 (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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46A LEU 3.3 15.5 - - - +
47A ASN 3.7 4.5 - - - +
48A VAL* 3.7 7.6 - - - -
49A GLY 3.4 26.0 - - - +
51A ILE* 1.4 92.9 - - + +
53A SER* 1.3 62.5 + - - +
55A ALA* 3.4 4.9 + - + +
56A LEU* 3.2 25.5 + - - +
92A LYS* 3.8 31.4 - - + +
96A VAL* 4.0 10.5 - - + -
172A LEU* 3.6 17.9 - - + -
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Residues in contact with SER 53 (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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49A GLY 2.8 24.9 + - - -
50A CYS* 2.9 2.9 + - - -
52A PRO* 1.3 75.3 - - - +
54A LYS* 1.3 90.8 + - - +
55A ALA 3.2 0.2 + - - -
56A LEU* 3.2 3.5 + - - +
57A LEU* 2.9 33.8 + - - +
172A LEU* 3.5 21.7 - - - +
192A GLU* 4.7 5.4 - - - -
193A LEU* 4.4 11.7 - - - -
196A VAL* 4.7 1.3 - - - +
480A FAD 3.9 9.6 - - - -
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Residues in contact with LYS 54 (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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50A CYS 2.8 22.3 + - - +
51A ILE* 3.8 3.1 - - - +
53A SER* 1.3 92.9 + - - +
55A ALA* 1.3 57.0 + - - +
57A LEU* 3.4 23.0 - - + +
58A ASN* 2.9 30.0 + - - +
192A GLU* 3.0 16.6 + - - -
359A TYR* 3.5 47.1 - - + -
480A FAD 2.9 27.8 + - - +
393B ARG* 5.3 6.3 - - + +
396B THR* 3.9 12.1 - - + +
397B ASN* 4.9 2.4 - - - +
453B PRO* 4.1 16.4 - - + -
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Residues in contact with ALA 55 (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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51A ILE* 3.1 7.9 + - + +
52A PRO* 3.5 10.8 - - + +
53A SER 3.1 0.6 - - - -
54A LYS* 1.3 74.0 - - - +
56A LEU* 1.3 67.0 + - - +
58A ASN* 3.0 4.8 + - - +
59A ASN* 2.9 29.4 + - - -
91A GLN* 3.8 17.5 - - - +
92A LYS* 4.1 20.0 - - + +
95A ALA* 5.5 2.0 - - + -
96A VAL* 6.3 0.2 - - + -
396B THR* 3.3 27.5 - - + +
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Residues in contact with LEU 56 (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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52A PRO 3.2 9.6 + - - +
53A SER* 3.2 8.4 + - - +
55A ALA* 1.3 78.5 - - - +
57A LEU* 1.3 52.1 + - - +
59A ASN* 4.6 2.7 - - - +
60A SER* 2.8 42.0 + - - -
88A MET* 4.3 26.8 - - + +
89A MET* 4.0 21.3 - - + -
92A LYS* 3.9 23.1 - - + -
172A LEU* 3.4 44.4 - - + +
193A LEU* 6.0 0.7 - - + -
196A VAL* 4.0 23.1 - - + -
197A TRP* 5.0 4.3 - - + +
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Residues in contact with LEU 57 (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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53A SER* 2.9 16.1 + - - +
54A LYS* 3.4 35.9 - - + +
56A LEU* 1.3 76.4 - - - +
58A ASN* 1.3 61.9 + - - +
60A SER* 3.1 6.8 + - - -
61A HIS* 3.2 5.5 + - - +
192A GLU* 3.8 30.7 - - + +
195A SER* 5.2 0.4 - - - -
196A VAL* 3.6 21.3 - - + +
199A ARG* 2.8 37.9 + - - +
359A TYR* 3.7 31.0 - - + +
360A THR* 4.2 9.9 - - + -
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Residues in contact with ASN 58 (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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54A LYS 2.9 17.1 + - - +
55A ALA* 3.0 5.8 + - - +
57A LEU* 1.3 78.7 - - - +
59A ASN* 1.3 62.6 + - - +
61A HIS* 3.4 6.3 + - - +
62A TYR* 3.1 55.3 + - - -
74B ARG* 3.4 27.1 - - - +
396B THR 5.0 0.6 + - - +
397B ASN* 3.4 39.7 + - - +
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Residues in contact with ASN 59 (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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55A ALA* 2.9 19.3 + - - +
56A LEU* 3.9 2.8 - - - +
58A ASN* 1.3 74.9 + - - +
60A SER* 1.3 59.9 + - - +
62A TYR* 3.1 7.2 + - - +
63A TYR* 2.8 28.4 + - - +
88A MET* 3.7 38.9 + - + +
91A GLN* 3.0 29.3 + - - +
92A LYS 4.9 0.2 - - - +
74B ARG* 2.7 48.9 + - + +
76B ILE* 3.7 4.2 - - - +
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Residues in contact with SER 60 (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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56A LEU 2.8 26.7 + - - -
57A LEU* 3.1 9.2 + - - -
59A ASN* 1.3 73.1 - - - +
61A HIS* 1.3 58.9 + - - +
63A TYR* 3.1 7.8 + - - +
64A HIS* 2.9 27.5 + - - +
88A MET* 3.9 11.1 - - - +
196A VAL* 3.8 28.2 - - - -
199A ARG* 3.1 20.6 + - - +
200A LEU* 3.9 11.9 - - - -
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Residues in contact with HIS 61 (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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57A LEU 3.2 15.0 + - - +
58A ASN* 3.7 6.1 - - - +
59A ASN 3.1 0.8 - - - -
60A SER* 1.3 82.6 + - - +
62A TYR* 1.3 82.7 + + - +
64A HIS* 3.2 10.5 + - - +
65A MET* 3.1 61.3 + - + +
199A ARG* 3.4 18.7 + - - +
361A HIS* 3.1 53.5 + + + +
62B TYR* 5.8 1.8 + - - -
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Residues in contact with TYR 62 (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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58A ASN* 3.1 49.9 + - - -
59A ASN* 3.1 9.9 + - - +
61A HIS* 1.3 94.4 - + - +
63A TYR* 1.3 65.9 + - - +
65A MET* 3.1 11.0 + - + +
66A ALA* 3.1 24.1 + - - +
71A PHE* 4.9 2.2 - + - -
61B HIS* 5.8 2.4 - + - -
62B TYR* 3.8 36.9 + + - -
65B MET* 6.5 0.4 - - + -
71B PHE* 3.6 37.3 - + + -
74B ARG* 5.0 8.3 - - - -
76B ILE* 3.7 9.2 - - + -
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Residues in contact with TYR 63 (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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59A ASN 2.8 13.3 + - - +
60A SER* 3.1 13.2 + - - +
62A TYR* 1.3 76.7 - - - +
64A HIS* 1.3 56.0 + - - +
66A ALA* 3.1 2.8 + - - +
67A HIS* 2.8 70.5 + + + +
81A VAL* 4.0 24.5 + - + -
82A ARG* 4.3 0.4 - - - -
83A LEU* 3.7 44.7 + - + +
88A MET* 5.2 2.0 - - - -
199A ARG 3.6 20.6 - - - -
200A LEU* 3.6 31.4 + - + -
76B ILE* 3.4 21.9 - - + +
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Residues in contact with HIS 64 (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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60A SER 2.9 11.5 + - - +
61A HIS* 3.2 16.9 + - - +
63A TYR* 1.3 82.6 - - - +
65A MET* 1.3 75.6 + - + +
67A HIS* 4.8 3.1 - + - -
68A GLY* 2.9 28.6 + - - +
70A ASP 5.3 0.2 + - - -
199A ARG* 4.7 26.3 + - + +
233A GLN* 4.9 19.0 + - + -
2000A SO4 2.9 37.5 + - - -
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Residues in contact with MET 65 (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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61A HIS* 3.1 44.9 + - + +
62A TYR* 3.1 12.3 + - + +
64A HIS* 1.3 113.7 - - + +
66A ALA* 1.3 59.8 + - - +
68A GLY 3.9 1.0 - - - +
70A ASP* 3.7 36.1 + - + +
71A PHE* 2.9 54.5 + - + +
361A HIS* 5.5 2.5 - - + -
2000A SO4 5.0 3.1 - - - +
62B TYR* 6.5 0.7 - - + -
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Residues in contact with ALA 66 (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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62A TYR 3.1 14.6 + - - +
63A TYR 3.6 2.7 - - - +
65A MET* 1.3 76.4 - - - +
67A HIS* 1.3 65.1 + - - +
68A GLY 3.3 6.8 - - - +
71A PHE* 4.2 4.7 - - + +
72A ALA 5.7 0.5 + - - -
78A MET* 3.5 28.8 - - + +
81A VAL* 3.5 15.1 - - + +
71B PHE* 4.0 11.7 - - + -
76B ILE* 3.9 22.2 - - + -
78B MET* 4.3 0.7 - - - -
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Residues in contact with HIS 67 (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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63A TYR* 2.8 50.6 + + + +
64A HIS* 4.6 3.6 - + - +
66A ALA* 1.3 75.7 - - - +
68A GLY* 1.3 62.7 + - - +
81A VAL* 3.7 36.8 + - + +
199A ARG 5.7 1.3 - - - -
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Residues in contact with GLY 68 (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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64A HIS* 2.9 20.9 + - - -
65A MET 3.9 2.1 - - - +
66A ALA 3.4 8.8 - - - +
67A HIS* 1.3 88.2 - - - +
69A THR* 1.3 65.2 + - - -
70A ASP 3.5 3.0 + - - -
71A PHE 4.7 0.3 + - - -
72A ALA* 4.7 6.1 + - - +
2000A SO4 3.8 14.8 - - - -
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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