Contacts of the strand formed by residues 126 - 133 (chain E) in PDB entry 5ZR1
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 126 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E ALA 4.8 1.8 - - - -
26E PRO* 3.9 4.2 - - - +
58E HIS* 4.3 16.6 - - + +
88E LEU* 5.9 0.7 - - + -
89E TYR* 3.9 24.5 + - + +
122E LEU* 4.9 5.1 - - - +
124E GLU* 3.3 17.0 + - - +
125E LYS* 1.3 78.4 + - - +
127E CYS* 1.3 70.5 + - - +
128E LEU* 4.2 1.3 + - + -
161E LYS 2.8 16.2 + - - +
162E ILE* 3.3 11.0 - - + -
163E ASN* 3.0 25.0 + - - +
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Residues in contact with CYS 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E SER 3.2 27.8 - - - -
24E ALA* 3.3 18.7 + - - -
26E PRO* 3.9 19.7 - - + +
29E THR* 4.8 1.8 - - - -
57E LEU* 5.6 1.3 - - - -
58E HIS* 4.3 11.1 + - - +
126E THR* 1.3 82.5 - - - +
128E LEU* 1.3 60.5 + - - +
129E PHE* 3.6 20.6 + - - -
163E ASN 3.3 13.0 - - - +
165E LYS* 3.9 14.8 - - + -
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Residues in contact with LEU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E HIS* 4.0 12.8 - - + +
60E VAL* 3.7 24.5 - - + -
81E VAL* 4.2 22.4 - - + +
84E LYS* 3.9 22.2 - - + -
85E LEU* 3.8 34.1 - - + -
88E LEU* 5.1 5.2 - - + -
116E PHE* 6.2 0.7 - - + -
126E THR* 4.2 2.1 + - + -
127E CYS* 1.3 72.5 - - - +
129E PHE* 1.3 69.2 + - - +
130E LEU* 3.6 2.2 + - + +
162E ILE* 4.4 15.0 - - + +
163E ASN 3.3 6.4 + - - +
164E ILE* 3.5 13.1 - - + -
165E LYS* 2.9 24.6 + - - -
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Residues in contact with PHE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ILE* 3.6 23.3 - - + -
23E SER 3.2 29.8 - - - -
29E THR* 3.8 22.7 - - + -
30E PRO 5.6 0.2 - - - -
51E PHE* 4.0 17.7 - + + -
57E LEU* 4.5 11.2 - - + -
58E HIS 3.0 28.0 + - - +
59E ALA* 3.3 1.5 - - - -
60E VAL* 2.7 32.7 + - - +
127E CYS* 3.6 20.6 - - - -
128E LEU* 1.3 73.6 - - - +
130E LEU* 1.3 57.1 - - - +
131E ILE* 3.6 3.6 + - + +
165E LYS* 3.4 18.4 - - + -
167E ILE* 3.6 31.0 - - + -
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Residues in contact with LEU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E VAL* 3.7 30.1 - - + +
62E LEU* 4.1 15.7 - - + -
77E ILE* 3.7 34.1 - - + -
80E THR* 4.7 1.1 - - - +
81E VAL* 3.8 19.3 - - + -
128E LEU* 3.6 2.1 + - + -
129E PHE* 1.3 69.2 - - - +
131E ILE* 1.3 59.8 + - - +
132E LEU* 3.4 7.7 + - + +
164E ILE* 3.7 18.4 - - + -
165E LYS 2.6 15.0 + - - +
166E PHE* 3.5 34.7 - - + -
167E ILE 3.1 19.5 + - - -
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Residues in contact with ILE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 3.8 22.7 - - + -
51E PHE* 3.7 26.9 - - + -
59E ALA* 3.8 14.4 - - + -
60E VAL 2.8 14.9 + - - +
61E TRP* 3.6 45.5 - - + -
62E LEU* 3.0 31.1 + - - +
129E PHE 4.1 6.1 - - - +
130E LEU* 1.3 70.9 - - - +
132E LEU* 1.3 62.0 + - - +
133E ASP* 4.2 9.4 - - + +
167E ILE* 3.5 28.0 - - + +
169E THR* 5.1 0.4 - - - +
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E LEU* 3.8 31.2 - - + -
64E PRO* 4.0 11.0 - - + -
73E LEU* 4.0 20.0 - - + -
77E ILE* 4.5 7.0 - - + -
130E LEU* 3.4 9.8 + - + +
131E ILE* 1.3 69.7 - - - +
133E ASP* 1.3 59.6 + - - +
134E GLY 3.3 2.8 + - - -
135E PHE* 3.8 24.3 + - + +
149E TYR* 4.4 14.1 - - + -
166E PHE* 4.3 12.6 - - + -
167E ILE 2.9 12.7 + - - +
168E TYR* 3.6 31.9 - - + -
169E THR 3.1 23.9 + - - -
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Residues in contact with ASP 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E THR* 3.2 34.7 - - - +
47E LEU* 4.0 10.9 - - - +
61E TRP* 4.0 15.7 - - + -
62E LEU 3.0 19.8 + - - +
63E GLU* 3.9 15.8 - - + +
64E PRO* 3.3 13.0 - - - +
65E VAL* 5.2 3.3 + - - +
131E ILE* 4.2 10.1 - - + -
132E LEU* 1.3 68.9 - - - +
134E GLY* 1.3 60.3 + - - +
169E THR* 3.5 17.9 + - - +
2002E MG 3.9 4.2 - - - -
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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