Contacts of the helix formed by residues 56 - 68 (chain D) in PDB entry 2ZPN
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 THR 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ASP 3.9 7.6 - - - +
55D LEU* 1.3 76.0 - - - +
57D VAL* 1.3 66.2 + - - +
58D GLY* 3.6 1.7 + - - -
59D GLN* 2.8 52.1 + - - +
60D PHE* 2.8 23.3 + - - +
87D THR 3.6 12.5 + - - -
88D ALA* 4.6 6.3 - - - +
89D ALA 3.4 7.4 - - - -
90D LEU* 4.0 16.2 - - + -
91D MET* 4.9 0.9 - - - -
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU 4.1 0.2 + - - -
56D THR* 1.3 70.8 - - - +
58D GLY* 1.3 59.2 - - - +
60D PHE* 2.9 9.6 + - - +
61D VAL* 2.8 45.2 + - + +
78D ILE* 4.3 13.2 - - + -
80D VAL* 6.1 0.2 - - + -
85D PRO* 3.8 27.6 - - + +
86D PRO 3.7 12.1 - - - +
87D THR* 3.5 5.5 + - + -
89D ALA* 2.9 23.9 + - + +
91D MET* 4.6 6.7 - - - -
94D ILE* 3.3 34.1 - - + -
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Residues in contact with GLY 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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59C GLN* 2.9 28.4 + - - -
56D THR* 3.8 1.3 - - - -
57D VAL* 1.3 72.8 - - - +
59D GLN* 1.3 60.8 + - - +
61D VAL* 3.5 9.0 + - - +
62D TYR 3.2 8.3 + - - -
87D THR* 2.7 40.4 + - - -
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Residues in contact with GLN 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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58C GLY* 3.3 30.8 + - - +
59C GLN* 4.3 8.5 - - + +
61C VAL* 5.2 2.6 - - - +
62C TYR* 3.4 32.8 - - + +
65C ARG* 6.1 1.2 - - - +
54D ASP 4.0 2.4 - - - +
55D LEU* 3.7 19.3 - - + +
56D THR* 2.8 55.5 + - - +
58D GLY* 1.3 70.8 - - - -
60D PHE* 1.3 66.4 + - - +
62D TYR* 3.3 11.0 + - - +
63D VAL* 3.2 25.7 + - - +
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Residues in contact with PHE 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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31D VAL* 4.3 14.8 - - + -
33D CYS* 3.8 36.1 - - + -
49D TYR* 4.3 7.6 - + + -
51D VAL* 3.8 11.4 - - + -
55D LEU* 3.5 25.7 - - + +
56D THR 2.8 12.3 + - - +
57D VAL* 3.2 13.5 - - - +
59D GLN* 1.3 78.5 - - - +
61D VAL* 1.3 61.2 + - - +
63D VAL* 3.3 7.2 + - - +
64D ILE* 3.3 30.6 + - + +
78D ILE* 3.0 31.2 - - + -
91D MET* 4.7 15.5 - - + -
107D VAL* 4.8 7.0 - - + -
4H LEU* 3.7 22.0 - - + -
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Residues in contact with VAL 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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59C GLN* 5.3 0.9 - - - +
57D VAL* 2.8 32.9 + - + +
58D GLY* 3.8 8.3 - - - +
59D GLN 3.2 0.2 - - - -
60D PHE* 1.3 73.2 - - - +
62D TYR* 1.3 66.1 + - - +
64D ILE* 3.3 4.3 + - - +
65D ARG* 3.0 23.2 + - - +
76D ILE* 3.5 37.9 - - + +
77D PHE* 5.1 0.2 - - - -
78D ILE* 3.3 33.0 - - + +
87D THR* 6.1 2.2 - - + -
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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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55C LEU* 3.6 22.2 - - + -
59C GLN* 3.1 36.7 - - + +
62C TYR* 4.4 15.3 - + - -
63C VAL* 3.5 28.8 - - + +
58D GLY 3.2 3.2 + - - +
59D GLN 3.4 11.0 - - - +
61D VAL* 1.3 80.2 - - - +
63D VAL* 1.3 64.1 + - + +
65D ARG* 3.4 8.9 + - + +
66D LYS* 3.2 50.6 + - + +
4G LEU* 2.8 44.8 + - - +
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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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62C TYR* 3.8 32.3 - - + +
49D TYR* 4.6 5.4 - - + -
55D LEU* 5.9 0.4 - - + -
59D GLN 3.2 15.5 + - - +
60D PHE* 3.4 9.4 - - - +
61D VAL 3.2 0.2 - - - -
62D TYR* 1.3 77.7 - - + +
64D ILE* 1.3 76.9 + - + +
65D ARG 3.3 0.2 + - - -
66D LYS* 3.3 5.4 + - - +
67D ARG* 3.2 28.3 + - + +
2H GLU* 5.0 1.3 - - - +
4H LEU* 4.0 35.7 - - + -
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Residues in contact with ILE 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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33D CYS* 3.9 21.3 - - - -
44D ILE* 5.3 4.9 - - + -
49D TYR* 4.0 26.5 - - + +
60D PHE* 3.4 33.7 - - + +
61D VAL* 3.3 7.5 + - + +
63D VAL* 1.3 82.1 - - + +
65D ARG* 1.3 62.8 + - - +
67D ARG* 3.2 15.1 + - + +
68D ILE* 3.2 17.7 + - + +
76D ILE* 3.4 24.2 - - + -
78D ILE* 4.6 5.8 - - + -
109D TYR* 4.1 24.9 - - + -
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Residues in contact with ARG 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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61D VAL* 3.0 18.6 + - - +
62D TYR* 3.6 11.0 - - - +
63D VAL 3.2 0.2 - - - -
64D ILE* 1.3 78.8 - - - +
66D LYS* 1.3 81.8 + - + +
68D ILE* 3.4 6.6 + - - +
69D MET* 3.2 17.7 + - - -
70D LEU* 3.4 29.3 + - + +
71D PRO 3.7 7.0 + - - -
72D PRO* 3.8 10.1 + - - +
74D LYS 2.5 32.1 + - - -
75D ALA* 3.5 7.5 - - - +
76D ILE* 2.9 46.2 + - + +
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Residues in contact with LYS 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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28C ARG* 5.2 3.0 - - - +
52C PRO* 4.1 10.1 - - - +
62D TYR* 3.2 43.1 + - + +
63D VAL* 3.3 4.5 + - - +
65D ARG* 1.3 92.8 - - + +
67D ARG* 1.3 65.6 + - - +
68D ILE 3.4 0.3 + - - -
69D MET* 3.5 11.3 + - - +
3G GLU* 6.0 1.1 - - + -
4G LEU* 3.0 37.5 + - - +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 4.3 30.6 - - + +
46D LYS* 2.9 35.6 - - - +
49D TYR* 3.9 14.4 + - - +
63D VAL* 3.2 21.5 + - + +
64D ILE* 3.2 12.3 + - - +
66D LYS* 1.3 79.0 - - - +
68D ILE* 1.3 60.2 + - - +
69D MET* 3.8 0.5 + - - +
2H GLU* 2.6 46.7 + - - +
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Residues in contact with ILE 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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41D ILE* 4.3 13.7 - - + -
42D PRO* 4.0 40.5 - - + +
44D ILE* 3.8 29.8 - - + -
64D ILE* 3.2 16.4 + - + +
65D ARG 3.6 7.6 - - - +
67D ARG* 1.3 79.3 - - - +
69D MET* 1.3 72.1 + - - +
70D LEU* 3.7 30.7 - - + +
76D ILE* 3.7 23.3 - - + -
109D TYR* 4.5 5.4 - - + +
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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
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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