Contacts of the helix formed by residues 49 - 68 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G THR 2.7 18.3 + - - -
45G CYS* 3.5 2.6 + - - -
48G VAL* 1.3 77.7 - - - +
50G CYS* 1.3 59.6 + - - -
51G ILE 3.3 1.7 + - - -
52G PRO* 3.3 4.7 - - - +
53G SER* 2.7 34.0 + - - -
172G LEU* 4.3 0.2 - - - +
480G FAD 3.4 25.4 - - - +
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Residues in contact with CYS 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G CYS* 2.0 51.8 + - - -
49G GLY* 1.3 70.2 - - - -
51G ILE* 1.3 63.0 + - + +
53G SER* 3.0 3.1 + - - -
54G LYS* 2.9 35.4 + - - +
328G ALA* 3.8 2.9 - - - -
480G FAD 3.3 58.0 - - + +
452H HIS* 4.1 1.1 - - + -
453H PRO* 4.3 10.8 - - + -
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Residues in contact with ILE 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G CYS 3.0 12.9 + - - +
46G LEU* 3.6 28.3 - - + +
50G CYS* 1.3 83.5 - - + +
52G PRO* 1.3 69.3 - - + +
54G LYS* 5.0 0.4 - - - -
55G ALA* 3.2 18.0 + - - +
92G LYS 5.4 0.2 - - - +
95G ALA* 4.6 3.4 - - + -
96G VAL* 3.8 24.7 - - + +
99G LEU* 3.7 29.2 - - + -
392H SER* 4.2 17.5 - - - +
396H THR* 3.2 30.1 - - + +
452H HIS* 4.5 8.3 - - - +
453H PRO* 4.7 6.1 - - + -
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Residues in contact with PRO 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LEU 3.5 12.8 - - - +
47G ASN 3.7 13.2 - - - +
49G GLY 3.3 19.7 - - - +
51G ILE* 1.3 96.1 - - + +
53G SER* 1.3 62.2 + - - +
55G ALA* 3.2 2.9 + - + +
56G LEU* 3.1 27.7 + - - +
92G LYS* 3.6 33.2 - - + +
96G VAL* 4.0 9.9 - - + -
172G LEU* 3.6 24.0 - - + -
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Residues in contact with SER 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLY 2.7 25.3 + - - -
50G CYS 3.0 3.8 + - - -
52G PRO* 1.3 78.6 - - - +
54G LYS* 1.3 85.0 + - - +
56G LEU* 3.2 3.7 + - - +
57G LEU* 2.8 32.7 + - - +
172G LEU* 3.6 19.6 - - - +
192G GLU* 4.4 3.6 - - - -
193G LEU* 4.0 15.7 - - - -
196G VAL* 4.7 0.9 - - - +
480G FAD 3.7 7.7 - - - -
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Residues in contact with LYS 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G CYS 2.9 21.2 + - - +
51G ILE* 5.0 0.2 - - - -
53G SER* 1.3 99.5 + - - +
55G ALA* 1.3 57.4 + - - +
57G LEU* 3.6 18.0 - - + +
58G ASN* 2.9 30.7 + - - +
192G GLU* 2.6 32.2 + - - -
359G TYR* 3.7 30.3 - - + -
480G FAD 3.0 35.5 + - - +
393H ARG* 5.5 6.5 - - + +
396H THR* 3.9 14.9 - - + +
397H ASN* 5.0 1.8 - - - +
453H PRO* 4.0 22.7 - - + -
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Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE 3.2 9.4 + - - +
52G PRO* 3.5 9.0 - - + +
53G SER 3.2 0.2 - - - -
54G LYS* 1.3 77.6 - - - +
56G LEU* 1.3 57.1 + - - +
58G ASN* 3.4 2.8 + - - +
59G ASN* 3.0 36.4 + - - +
91G GLN* 3.7 18.4 - - - +
92G LYS* 3.9 20.6 - - + +
95G ALA* 5.1 2.0 - - + -
396H THR* 3.3 25.7 - - + +
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Residues in contact with LEU 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G PRO 3.1 12.5 + - - +
53G SER* 3.8 3.1 - - - +
55G ALA* 1.3 73.3 - - - +
57G LEU* 1.3 65.1 + - - +
59G ASN* 4.1 2.6 - - - +
60G SER* 2.7 32.7 + - - -
88G MET* 4.2 27.1 - - + +
89G MET* 3.9 21.5 - - + -
92G LYS* 4.1 23.6 - - + -
171G ALA 4.9 2.5 - - - +
172G LEU* 3.5 44.6 - - + +
193G LEU* 5.8 0.7 - - + -
196G VAL* 3.9 25.8 - - + -
197G TRP* 5.1 0.9 - - + +
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Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G SER* 2.8 17.1 + - - +
54G LYS* 3.6 36.3 - - + +
56G LEU* 1.3 78.3 - - - +
58G ASN* 1.3 61.3 + - - +
60G SER* 3.6 2.7 - - - -
61G HIS* 3.1 10.4 + - - +
192G GLU* 3.6 38.1 - - + +
195G SER* 4.8 0.7 - - - -
196G VAL* 3.8 10.5 - - + +
199G ARG* 2.8 42.8 + - - +
359G TYR* 3.5 32.5 - - + +
360G THR* 4.1 6.7 - - - -
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Residues in contact with ASN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G LYS 2.9 18.3 + - - +
55G ALA* 3.7 5.8 - - - +
57G LEU* 1.3 75.6 - - - +
59G ASN* 1.3 64.6 + - - +
61G HIS* 3.3 8.8 + - - +
62G TYR* 3.1 63.1 + - - -
74H ARG* 3.5 21.8 + - - -
396H THR 5.6 0.4 - - - +
397H ASN* 3.5 34.8 + - - +
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Residues in contact with ASN 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ALA 3.0 21.4 + - - +
56G LEU* 4.1 3.7 - - - +
58G ASN* 1.3 76.7 - - - +
60G SER* 1.3 58.6 + - - +
62G TYR* 3.4 6.4 + - - +
63G TYR* 3.0 27.0 + - - +
88G MET* 3.5 47.1 + - + +
91G GLN* 2.7 27.6 + - - +
92G LYS 4.6 0.4 - - - +
74H ARG* 2.9 44.0 + - + +
76H ILE* 3.8 2.4 - - - +
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LEU 2.7 27.4 + - - -
57G LEU* 3.6 1.4 - - - -
59G ASN* 1.3 70.6 - - - +
61G HIS* 1.3 64.4 + - - +
63G TYR* 3.4 2.6 + - - +
64G HIS* 3.1 22.9 + - - +
88G MET* 4.4 1.7 - - - +
196G VAL* 3.7 25.3 - - - -
199G ARG* 2.9 40.5 + - - +
200G LEU* 3.8 22.9 - - - -
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Residues in contact with HIS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU 3.1 20.5 + - - +
58G ASN* 3.7 7.6 - - - +
60G SER* 1.3 78.1 + - - +
62G TYR* 1.3 82.8 + + - +
64G HIS* 3.2 8.8 + - - +
65G MET* 2.9 65.1 + - + +
199G ARG* 3.6 16.9 - - - +
361G HIS* 3.4 51.3 + + + +
62H TYR* 5.9 0.8 + - - -
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Residues in contact with TYR 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G ASN* 3.1 56.9 + - - +
59G ASN* 3.8 1.8 - - - +
60G SER 3.3 0.2 - - - -
61G HIS* 1.3 95.7 - + - +
63G TYR* 1.3 61.0 + - - +
65G MET* 3.2 11.6 + - + +
66G ALA* 3.0 24.6 + - - +
61H HIS* 5.6 2.8 + - - -
62H TYR* 4.2 28.0 + + - -
65H MET* 6.4 1.3 - - + -
70H ASP* 5.6 0.9 - - - -
71H PHE* 3.6 30.5 - + + -
74H ARG* 4.4 18.6 - - - -
76H ILE* 3.5 13.2 - - + -
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Residues in contact with TYR 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ASN 3.0 13.4 + - - +
60G SER* 3.4 10.8 - - - +
62G TYR* 1.3 75.5 - - - +
64G HIS* 1.3 55.3 + - - +
66G ALA* 3.2 1.7 + - - +
67G HIS* 2.8 80.7 + + + +
81G VAL* 4.1 10.6 + - + -
82G ARG* 4.2 2.0 - - - -
83G LEU* 4.0 37.7 + - + +
88G MET* 4.3 4.9 - - + -
199G ARG 3.5 26.5 - - - -
200G LEU* 3.7 27.0 + - + -
76H ILE* 3.3 30.2 - - + +
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Residues in contact with HIS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G SER 3.1 10.3 + - - +
61G HIS* 3.3 12.3 + - - +
63G TYR* 1.3 86.1 - - + +
65G MET* 1.3 74.4 + - + +
67G HIS* 4.6 4.5 - - - -
68G GLY* 2.8 29.3 + - - -
70G ASP 5.3 0.2 + - - -
199G ARG* 4.3 27.7 + - + +
233G GLN* 5.5 14.1 - - + -
2023G SO4 2.9 43.4 + - - -
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Residues in contact with MET 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G HIS* 2.9 51.5 + - + +
62G TYR* 3.2 14.1 + - + +
64G HIS* 1.3 115.1 - - + +
66G ALA* 1.3 59.8 + - - +
68G GLY 4.2 0.9 - - - +
70G ASP* 3.5 33.4 + - + +
71G PHE* 3.0 48.6 + - + -
361G HIS* 5.7 2.7 - - + +
2023G SO4 4.7 3.6 - - - +
62H TYR* 6.3 1.6 - - + -
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Residues in contact with ALA 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G TYR 3.0 16.4 + - - +
63G TYR 3.7 3.1 - - - +
65G MET* 1.3 78.5 - - - +
67G HIS* 1.3 61.8 + - - +
68G GLY 3.3 6.5 + - - +
71G PHE* 4.1 3.6 - - + +
78G MET* 3.3 34.3 - - + +
81G VAL* 3.5 12.6 - - + +
71H PHE* 3.8 20.6 - - + -
76H ILE* 3.9 15.7 - - + -
78H MET* 4.6 0.4 - - + -
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Residues in contact with HIS 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G TYR* 2.8 55.3 + + + +
64G HIS* 4.4 3.0 - - - +
66G ALA* 1.3 73.4 - - - +
68G GLY* 1.3 61.9 + - - +
81G VAL* 3.5 37.4 + - + -
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Residues in contact with GLY 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G HIS* 2.8 19.5 + - - +
65G MET 4.2 1.9 - - - +
66G ALA 3.3 8.0 - - - +
67G HIS* 1.3 85.7 + - - +
69G THR* 1.3 63.9 + - - -
70G ASP 3.5 3.0 + - - -
71G PHE 4.7 1.2 + - - -
72G ALA* 4.8 7.4 + - - +
2023G SO4 3.1 16.4 - - - -
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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