Contacts of the helix formed by residues 58 - 74 (chain D) in PDB entry 1ZVM
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 ARG 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A THR* 4.1 15.0 - - - +
57A LYS 3.6 18.2 - - - +
58A ARG* 3.8 13.2 - - + -
62A THR* 3.7 16.1 + - - +
66A ARG* 4.0 17.4 - - - +
156A ASP* 5.1 5.7 + - - +
157A LEU* 3.8 25.2 - - - +
56D THR 3.5 0.4 + - - -
57D LYS* 1.3 99.2 - - + +
59D PHE* 1.3 60.7 + - - +
60D PRO* 3.4 4.0 - - - -
61D GLU* 3.2 34.8 + - + +
62D THR* 2.5 33.2 + - - +
170D TYR* 4.3 6.6 + - - -
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Residues in contact with PHE 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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55D THR* 3.6 13.5 - - + -
56D THR* 3.2 23.0 + - - +
57D LYS 3.2 2.0 - - - -
58D ARG* 1.3 76.7 - - - +
60D PRO* 1.3 72.3 - - + +
62D THR* 3.1 4.3 + - - -
63D VAL* 3.1 39.1 + - + +
86D TRP* 3.8 26.2 - + - -
89D PHE* 4.1 11.2 - + - -
93D PHE* 4.3 11.9 - + - -
157D LEU* 3.4 35.2 - - + -
158D THR 4.2 7.0 - - - -
159D TRP* 3.4 51.4 - + + -
168D ILE* 4.8 2.2 - - + -
170D TYR* 4.6 0.4 + - - +
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Residues in contact with PRO 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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58D ARG* 3.6 2.9 - - - -
59D PHE* 1.3 95.9 - - + +
61D GLU* 1.3 72.3 + - + +
63D VAL* 3.4 2.1 + - - +
64D LEU* 3.2 23.6 + - - +
86D TRP* 3.5 44.0 - - + +
168D ILE* 3.8 13.5 - - + -
170D TYR* 3.6 15.5 - - - +
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Residues in contact with GLU 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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61A GLU* 3.5 2.6 - - + +
62A THR* 3.9 30.1 - - + +
65A ALA* 3.5 26.2 - - + +
66A ARG* 5.2 6.4 + - + -
58D ARG* 3.2 54.0 + - + +
60D PRO* 1.3 85.6 - - + +
62D THR* 1.3 57.8 + - - +
65D ALA* 2.9 32.1 + - - +
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Residues in contact with THR 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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58A ARG* 3.5 43.0 + - - +
61A GLU* 4.0 16.0 - - + +
56D THR* 5.5 0.6 - - - +
57D LYS 4.4 0.2 + - - -
58D ARG 2.5 23.7 + - - -
59D PHE* 3.1 6.9 + - - -
61D GLU* 1.3 76.3 - - - +
63D VAL* 1.3 59.8 + - - +
65D ALA* 4.0 0.3 - - - +
66D ARG* 3.0 61.3 + - - +
157D LEU* 4.2 11.0 - - + -
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Residues in contact with VAL 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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59D PHE* 3.1 46.4 + - + +
62D THR* 1.3 75.1 - - - +
64D LEU* 1.3 61.2 + - - +
66D ARG* 4.4 3.6 - - - -
67D CYS* 3.0 27.7 + - - +
85D VAL* 5.0 3.1 - - + -
86D TRP* 3.8 30.1 - - + -
89D PHE* 3.8 26.2 - - + -
153D LEU* 3.7 29.8 - - + +
157D LEU* 4.3 0.9 - - + -
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Residues in contact with LEU 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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65A ALA* 3.8 32.3 - - + +
68A VAL* 4.2 19.7 - - + -
69A LYS* 4.7 8.1 - - + +
60D PRO 3.2 16.1 + - - +
61D GLU 4.1 2.7 - - - +
63D VAL* 1.3 76.2 - - - +
65D ALA* 1.3 65.8 + - - +
67D CYS* 3.3 3.1 + - - +
68D VAL* 3.0 30.4 + - + +
82D CYS* 3.6 42.0 - - + +
83D GLN* 4.0 24.0 - - - +
86D TRP* 4.8 10.7 - - + -
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Residues in contact with ALA 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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61A GLU* 3.5 39.5 - - + +
64A LEU* 3.7 23.8 - - + +
65A ALA* 4.4 2.6 - - - +
61D GLU 2.9 19.7 + - - +
62D THR 4.0 0.4 - - - +
64D LEU* 1.3 76.7 - - - +
66D ARG* 1.3 57.3 + - - +
68D VAL* 3.4 2.4 + - - +
69D LYS* 2.8 31.9 + - - +
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Residues in contact with ARG 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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58A ARG* 3.9 19.2 - - - +
61A GLU* 5.3 3.5 + - + -
62D THR* 3.0 35.3 + - + +
63D VAL 3.8 4.0 - - - +
65D ALA* 1.3 74.9 - - + +
67D CYS* 1.3 56.7 + - - +
69D LYS* 3.2 2.8 + - - -
70D TYR* 2.7 37.8 + - - +
152D TYR* 3.3 44.7 + - + +
153D LEU* 3.1 34.0 + - + -
155D ASP* 2.9 31.2 + - - +
156D ASP* 4.9 4.4 + - - +
157D LEU* 3.2 17.9 - - - +
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Residues in contact with CYS 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 VAL* 3.0 18.9 + - + +
64D LEU* 3.7 2.2 - - - +
66D ARG* 1.3 75.3 - - - +
68D VAL* 1.3 56.7 + - - +
70D TYR* 3.6 0.7 - - - +
71D THR* 2.9 37.6 + - - +
80D VAL* 4.0 15.9 - - - -
82D CYS* 2.0 55.2 - - + +
85D VAL* 4.2 11.7 - - + -
149D LEU* 4.3 10.1 - - - -
153D LEU* 3.3 17.4 - - + +
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Residues in contact with VAL 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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64A LEU* 4.1 19.1 - - + -
68A VAL* 3.9 33.2 - - + -
82A CYS* 5.9 1.6 - - + -
83A GLN* 6.0 2.2 - - + +
64D LEU* 3.0 23.3 + - + +
65D ALA* 3.6 5.2 - - - +
67D CYS* 1.3 75.9 - - - +
69D LYS* 1.3 61.6 + - - +
71D THR* 2.9 19.6 + - - +
72D GLU* 3.2 19.5 + - + +
82D CYS* 3.8 17.7 - - + -
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Residues in contact with LYS 69 (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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64A LEU* 4.6 5.1 - - + +
83A GLN* 4.0 23.0 + - - +
86A TRP* 6.4 0.2 - - - -
65D ALA 2.8 21.1 + - - +
66D ARG* 3.6 6.1 - - - +
68D VAL* 1.3 73.5 - - - +
70D TYR* 1.3 61.1 + - - +
72D GLU* 2.8 50.5 + - - +
73D ILE* 3.2 30.1 + - + +
152D TYR* 4.3 14.1 - - - +
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Residues in contact with TYR 70 (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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66D ARG 2.7 20.7 + - - +
67D CYS 3.6 3.8 - - - +
69D LYS* 1.3 73.1 - - - +
71D THR* 1.3 60.7 + - - +
73D ILE* 3.1 7.2 + - + -
74D HIS* 2.9 67.7 + + + -
77D MET* 4.2 8.7 - - + -
115D GLN* 2.9 24.2 + - - -
143D PHE* 4.7 1.0 - - - -
147D ASP 2.9 25.1 + - - -
148D THR 3.5 6.7 - - - -
149D LEU* 3.1 45.8 + - + -
152D TYR* 3.6 34.9 - + + -
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Residues in contact with THR 71 (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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67D CYS* 2.9 19.4 + - - +
68D VAL* 2.9 21.5 + - - +
70D TYR* 1.3 79.3 - - + +
72D GLU* 1.3 58.4 + - - +
74D HIS 3.1 22.9 - - - +
75D PRO* 3.9 4.7 - - - +
77D MET* 3.5 29.4 - - + +
78D ARG* 4.3 11.3 + - - +
80D VAL* 4.0 20.4 + - + +
82D CYS* 4.1 11.2 - - - -
149D LEU* 5.1 2.7 - - + -
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Residues in contact with GLU 72 (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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83A GLN* 3.3 41.3 + - - +
68D VAL* 3.2 15.5 + - + +
69D LYS* 2.8 51.9 + - - +
70D TYR 3.1 1.0 - - - -
71D THR* 1.3 77.0 + - - +
73D ILE* 1.3 70.5 + - + +
74D HIS 3.6 0.2 + - - -
75D PRO* 4.0 10.9 - - - +
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Residues in contact with ILE 73 (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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69D LYS* 3.3 37.9 - - + +
70D TYR* 3.1 7.5 + - + +
72D GLU* 1.3 85.0 - - + +
74D HIS* 1.3 81.7 + - + +
75D PRO* 3.0 11.6 - - - +
152D TYR* 5.1 8.7 - - + +
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Residues in contact with HIS 74 (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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70D TYR* 2.9 61.4 + + + +
71D THR 3.1 13.1 - - - +
73D ILE* 1.3 98.6 - - + +
75D PRO* 1.3 68.4 - - - +
76D GLU* 3.0 8.1 - - + +
77D MET* 2.9 19.7 + - + +
115D GLN* 5.0 3.1 - - - -
143D PHE* 4.8 15.8 - + - -
147D ASP 4.6 5.3 + - - -
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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