Contacts of the strand formed by residues 41 - 47 (chain H) in PDB entry 2ZHX
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 ILE 41 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ILE 3.5 1.0 - - - +
23H LEU* 3.2 7.3 - - - -
24H MET* 2.7 40.7 + - - +
25H LEU 5.1 0.4 - - - -
29H VAL* 4.1 17.9 - - + -
37H PRO* 3.6 25.6 - - + -
39H SER 4.0 6.5 - - - +
40H ASP* 1.3 78.3 - - - +
42H LEU* 1.3 73.7 + - - +
43H VAL* 3.9 3.3 + - + +
58H LEU* 3.8 21.1 - - + -
59H THR 3.3 15.7 - - - +
60H SER* 5.0 1.3 - - - -
68H TRP* 3.4 41.7 - - + -
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G GLN* 5.0 0.2 - - - +
137G PRO* 5.0 3.6 - - + -
138G ALA* 4.5 17.0 - - + -
141G ARG* 5.0 1.6 - - - +
21H SER* 3.6 29.2 - - - +
22H ILE 3.3 0.4 - - - -
23H LEU* 3.7 32.8 - - + +
41H ILE* 1.3 73.9 - - - +
43H VAL* 1.3 60.0 + - - +
44H HIS* 3.2 28.6 + - + +
58H LEU* 3.3 4.5 - - - -
59H THR 2.9 31.0 + - - -
60H SER 3.6 18.8 + - - +
61H ASP* 4.0 17.3 - - - +
62H ALA* 4.1 7.9 - - - +
65H TYR* 4.5 9.6 - - + -
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Residues in contact with VAL 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G SER* 4.3 7.0 - - - +
195G LEU* 3.8 43.1 - - + -
20H GLU 3.5 2.6 - - - +
22H ILE* 2.6 41.6 + - + +
24H MET* 3.8 20.0 - - + -
29H VAL* 5.5 0.2 - - + -
41H ILE* 4.4 11.7 - - + -
42H LEU* 1.3 70.5 - - - +
44H HIS* 1.3 64.3 + - - +
45H THR* 3.3 18.2 + - - +
56H MET* 4.2 15.9 - - + -
57H LEU 4.2 1.8 - - - -
58H LEU* 4.2 9.9 - - + -
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Residues in contact with HIS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G PRO* 3.9 14.4 - - + +
4H LEU* 3.7 27.6 - - + +
8H ILE* 5.7 0.7 - - + -
18H ILE* 3.7 31.4 - - + -
20H GLU 3.2 7.2 - - - -
21H SER* 3.1 19.7 + - - -
42H LEU* 3.2 27.5 + - + +
43H VAL* 1.3 71.7 - - - +
45H THR* 1.3 59.1 + - - +
46H ALA 4.3 0.2 - - - -
55H VAL 3.7 0.7 - - - +
56H MET* 3.1 5.0 - - - -
57H LEU* 2.8 47.4 + - + +
59H THR* 3.1 29.6 + - + -
65H TYR* 4.5 1.6 - - - -
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Residues in contact with THR 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ARG* 4.2 13.9 + - + +
193G SER* 4.0 7.1 + - - -
194G PRO* 3.7 27.8 - - + -
18H ILE* 4.5 2.1 - - - +
19H GLN* 3.1 29.1 + - - +
20H GLU* 3.1 28.0 + - - +
43H VAL* 3.3 11.1 + - - +
44H HIS* 1.3 77.9 + - - +
46H ALA* 1.3 65.5 + - - +
54H ASN* 4.6 4.7 - - + -
55H VAL 3.4 4.0 - - - +
56H MET* 3.5 20.7 - - + +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ARG* 5.3 0.2 - - - -
8H ILE* 4.8 6.7 - - + -
16H LEU* 4.1 20.4 - - + -
17H VAL 3.1 32.1 - - - +
18H ILE* 3.9 9.1 - - + +
19H GLN* 4.5 1.3 - - - +
44H HIS 4.3 0.2 - - - -
45H THR* 1.3 77.1 - - - +
47H TYR* 1.3 59.7 + - - +
54H ASN* 3.8 1.4 - - - -
55H VAL* 2.8 39.2 + - + +
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Residues in contact with TYR 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G PRO* 4.6 14.8 - - + +
92G ARG* 3.4 55.4 - - + -
16H LEU* 3.2 16.5 - - - +
17H VAL 4.6 1.6 + - - -
19H GLN* 4.2 15.2 + - - +
46H ALA* 1.3 75.4 - - - +
48H ASP* 1.3 64.0 + - - +
49H GLU* 3.5 49.0 + - + +
52H ASP* 2.8 34.6 + - - +
53H GLU 3.2 28.5 - - - -
54H ASN* 3.7 8.7 - - - +
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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