Contacts of the helix formed by residues 49 - 68 (chain B) in PDB entry 1ZMD
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B THR 2.7 17.7 + - - -
45B CYS 3.6 1.4 + - - -
48B VAL* 1.3 79.7 - - - +
50B CYS* 1.3 60.6 + - - -
51B ILE 3.4 1.6 - - - -
52B PRO* 3.1 5.3 - - - +
53B SER* 2.7 33.6 + - - -
480B FAD 3.3 25.6 - - - +
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Residues in contact with CYS 50 (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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452A HIS* 4.0 2.9 - - + -
453A PRO* 4.5 9.2 - - + -
45B CYS* 2.0 53.7 + - - -
49B GLY* 1.3 69.2 - - - -
51B ILE* 1.3 63.3 + - + +
53B SER* 3.0 1.7 + - - -
54B LYS* 2.9 35.6 + - - +
328B ALA* 3.9 1.3 - - - -
480B FAD 3.3 57.5 - - + +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A SER* 4.1 17.0 - - - -
396A THR* 3.4 30.5 - - - +
452A HIS* 4.7 4.7 - - - +
453A PRO* 4.9 5.4 - - + -
45B CYS 3.0 6.8 + - - +
46B LEU* 3.3 36.3 - - + +
50B CYS* 1.3 87.9 - - + +
52B PRO* 1.3 69.8 - - + +
54B LYS* 4.9 0.9 - - + -
55B ALA* 3.0 19.4 + - - +
95B ALA* 4.3 6.1 - - + -
96B VAL* 3.9 24.7 - - + +
99B LEU* 3.5 27.6 - - + -
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Residues in contact with PRO 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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45B CYS 3.8 0.2 - - - +
46B LEU 3.4 14.6 - - - +
47B ASN 3.9 3.8 - - - +
48B VAL* 3.7 10.8 - - - -
49B GLY 3.1 32.5 - - - +
51B ILE* 1.3 94.5 - - + +
53B SER* 1.3 60.4 + - - +
55B ALA* 3.3 3.2 + - + +
56B LEU* 3.0 27.4 + - - +
92B LYS* 3.8 30.5 - - + +
96B VAL* 4.0 9.9 - - + -
172B LEU* 3.7 15.0 - - + -
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY 2.7 25.5 + - - -
50B CYS 3.0 3.3 + - - -
52B PRO* 1.3 78.7 - - - +
54B LYS* 1.3 86.6 + - - +
56B LEU* 3.2 4.0 + - - +
57B LEU* 2.7 34.0 + - - +
172B LEU* 3.6 19.7 - - - +
192B GLU* 4.6 3.8 - - - -
193B LEU* 4.2 13.9 - - - -
196B VAL* 4.7 0.5 - - - +
480B FAD 3.6 9.0 - - - -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 5.5 7.0 - - + +
396A THR* 4.0 12.1 - - + -
397A ASN* 5.2 3.7 - - - +
453A PRO* 3.9 21.5 - - + -
50B CYS 2.9 20.5 + - - +
51B ILE* 4.0 2.9 - - - +
53B SER* 1.3 104.1 + - - +
55B ALA* 1.3 58.0 + - - +
57B LEU* 3.6 21.7 - - + +
58B ASN* 2.8 31.7 + - - +
192B GLU* 3.0 21.2 + - - -
359B TYR* 3.7 30.3 - - + -
480B FAD 3.0 34.7 + - - +
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Residues in contact with ALA 55 (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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396A THR* 3.4 25.3 - - + +
51B ILE 3.0 13.7 + - - +
52B PRO* 3.6 4.9 - - + +
53B SER 3.2 0.2 - - - -
54B LYS* 1.3 75.1 - - - +
56B LEU* 1.3 58.0 + - - +
58B ASN* 3.3 6.6 + - - +
59B ASN* 2.9 36.5 + - - -
91B GLN* 3.9 15.7 - - - +
92B LYS* 3.9 22.4 - - + +
95B ALA* 5.0 1.6 - - + -
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Residues in contact with LEU 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 PRO 3.0 16.5 + - - +
53B SER* 3.8 4.0 - - - +
55B ALA* 1.3 73.3 - - - +
57B LEU* 1.3 58.0 + - - +
59B ASN* 4.5 1.8 - - - +
60B SER* 2.7 38.9 + - - -
88B MET* 4.4 25.9 - - + +
89B MET* 3.8 21.5 - - + -
92B LYS* 4.1 23.6 - - + -
171B ALA 4.8 2.7 - - - +
172B LEU* 3.4 44.6 - - + +
193B LEU* 5.8 0.9 - - + -
196B VAL* 3.9 24.2 - - + -
197B TRP* 5.0 1.3 - - + +
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Residues in contact with LEU 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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53B SER* 2.7 21.6 + - - +
54B LYS* 3.2 36.1 + - - +
56B LEU* 1.3 72.7 - - - +
58B ASN* 1.3 60.9 + - - +
60B SER* 3.0 7.1 + - - -
61B HIS* 3.1 6.4 + - - +
192B GLU* 3.6 34.5 - - + +
193B LEU* 5.8 0.2 - - + -
195B SER* 4.8 0.9 - - - -
196B VAL* 3.4 21.1 - - + +
199B ARG* 2.8 38.1 + - - +
359B TYR* 3.6 34.3 - - + +
360B THR* 4.5 1.3 - - - -
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Residues in contact with ASN 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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74A ARG* 3.2 24.3 + - - -
393A ARG* 6.0 1.0 - - - +
396A THR 5.4 0.4 - - - +
397A ASN* 3.2 40.9 - - - +
54B LYS 2.8 18.3 + - - +
55B ALA* 3.4 7.2 - - - +
57B LEU* 1.3 78.1 - - - +
59B ASN* 1.3 63.2 + - - +
61B HIS* 3.4 7.2 + - - +
62B TYR* 3.1 51.0 + - - -
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Residues in contact with ASN 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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74A ARG* 2.9 44.9 + - + +
76A ILE* 3.7 6.6 - - - +
55B ALA 2.9 23.5 + - - +
56B LEU* 4.2 2.7 - - - +
58B ASN* 1.3 70.2 - - - +
60B SER* 1.3 61.2 + - - +
62B TYR* 3.3 5.2 + - - -
63B TYR* 2.9 28.2 + - - +
88B MET* 3.5 44.4 + - + +
91B GLN* 2.6 28.0 + - - +
92B LYS 4.6 0.4 - - - +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 2.7 22.9 + - - -
57B LEU* 3.6 1.9 - - - -
59B ASN* 1.3 74.6 - - - +
61B HIS* 1.3 64.3 + - - +
63B TYR* 3.3 2.5 + - - +
64B HIS* 2.9 22.9 + - - +
88B MET* 4.4 1.4 - - - -
196B VAL* 3.8 23.9 - - - -
199B ARG* 3.0 36.7 + - - +
200B LEU* 3.9 23.1 - - - -
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 5.7 3.2 + - - -
57B LEU 3.1 15.0 + - - +
58B ASN* 3.7 5.8 - - - +
59B ASN 3.3 0.4 - - - -
60B SER* 1.3 83.0 + - - +
62B TYR* 1.3 79.5 + + - +
64B HIS* 3.2 8.8 + - - +
65B MET* 3.0 71.0 + - + +
199B ARG* 3.6 16.5 - - - +
361B HIS* 3.6 48.5 - + + +
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Residues in contact with TYR 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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62A TYR* 4.7 21.5 - + - -
65A MET* 5.6 7.1 - - + +
70A ASP* 5.1 0.9 - - - -
71A PHE* 3.6 33.3 - + + -
74A ARG* 3.7 33.4 + - - -
76A ILE* 3.6 17.9 - - + -
397A ASN* 5.5 1.6 + - - +
58B ASN* 3.1 44.4 + - - -
59B ASN 3.7 3.1 - - - +
60B SER 3.3 0.2 - - - -
61B HIS* 1.3 94.1 - + - +
63B TYR* 1.3 65.4 + - - +
65B MET* 3.3 8.2 + - + +
66B ALA* 3.1 17.8 + - - +
71B PHE* 5.8 0.2 - + - -
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Residues in contact with TYR 63 (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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76A ILE* 3.4 22.6 - - + +
59B ASN 2.9 14.9 + - - +
60B SER* 3.5 11.0 - - - +
62B TYR* 1.3 74.5 - - - +
64B HIS* 1.3 55.6 + - - +
66B ALA* 3.2 1.2 + - - +
67B HIS* 2.7 75.0 + + + +
81B VAL* 4.0 22.4 + - + -
82B ARG* 4.0 0.8 - - - -
83B LEU* 3.7 44.5 + - + +
88B MET* 4.2 4.5 - - + -
199B ARG 3.6 25.6 - - - -
200B LEU* 3.8 23.6 + - + -
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Residues in contact with HIS 64 (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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60B SER 2.9 12.8 + - - +
61B HIS* 3.2 15.8 + - - +
63B TYR* 1.3 82.2 - - - +
65B MET* 1.3 76.0 + - + +
67B HIS* 4.7 2.0 - - - -
68B GLY* 2.8 29.8 + - - +
70B ASP 5.3 0.2 + - - -
199B ARG* 4.4 25.1 + - + +
233B GLN* 5.6 14.6 - - + -
361B HIS* 6.2 1.1 - + - -
2003B SO4 2.6 38.7 + - - -
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Residues in contact with MET 65 (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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62A TYR* 6.4 2.2 - - + -
61B HIS* 3.0 49.4 + - + +
62B TYR* 3.3 12.5 + - + +
64B HIS* 1.3 114.8 - - + +
66B ALA* 1.3 61.6 + - - +
68B GLY 4.1 0.9 + - - +
70B ASP* 3.7 31.5 + - + +
71B PHE* 3.1 50.6 + - + +
361B HIS* 5.4 3.8 - - + -
2003B SO4 5.4 2.7 - - - +
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Residues in contact with ALA 66 (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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71A PHE* 3.7 22.7 - - + -
76A ILE* 4.1 11.9 - - + -
78A MET* 4.3 0.9 - - - -
62B TYR 3.1 15.9 + - - +
63B TYR 3.7 2.5 - - - +
65B MET* 1.3 77.0 - - - +
67B HIS* 1.3 65.5 + - - +
68B GLY 3.4 7.4 + - - +
71B PHE* 4.1 7.1 - - + +
72B ALA 5.7 0.2 + - - -
78B MET* 3.2 36.6 - - + +
81B VAL* 3.8 6.9 - - + +
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Residues in contact with HIS 67 (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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63B TYR* 2.7 59.0 + + + +
64B HIS* 4.5 1.8 - - - +
66B ALA* 1.3 74.0 - - - +
68B GLY* 1.3 62.1 + - - +
81B VAL* 3.4 38.0 + - + +
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Residues in contact with GLY 68 (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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64B HIS* 2.8 23.9 + - - +
65B MET 4.1 1.6 - - - +
66B ALA 3.3 8.3 - - - +
67B HIS* 1.3 86.2 + - - +
69B THR* 1.3 63.2 + - - -
70B ASP 3.6 2.2 + - - -
71B PHE 4.9 0.7 + - - -
72B ALA* 5.0 5.5 + - - +
2003B SO4 3.3 10.5 - - - -
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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