Contacts of the strand formed by residues 150 - 158 (chain E) in PDB entry 1ZUM
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 PHE 150 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ILE 5.5 0.7 - - - +
146E ILE* 3.7 22.6 + - + +
147E ASP 3.5 17.3 - - - -
148E GLY* 3.0 10.7 + - - +
149E ASP* 1.3 90.9 - - + +
151E PHE* 1.3 62.1 + - - +
152E SER 4.1 0.7 + - - -
492E THR* 4.0 4.9 - - + -
493E VAL 3.1 8.7 - - - +
494E LYS* 3.7 23.3 - - + -
495E VAL* 3.7 8.8 - - - +
498E LYS* 4.3 12.8 - - - +
3102E GAI 3.5 20.9 - - - -
285F TRP* 6.5 0.2 - + - -
455F CYS* 3.9 20.2 - - + -
458F VAL* 3.8 36.1 - - + -
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Residues in contact with PHE 151 (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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143E THR* 4.0 18.2 - - + -
144E ILE 5.9 0.4 - - - -
150E PHE* 1.3 74.4 - - - +
152E SER* 1.3 69.0 + - - +
153E TYR* 3.4 34.9 - + + -
491E VAL 3.8 1.4 - - - +
492E THR* 3.5 0.9 - - - -
493E VAL* 2.8 42.6 + - + +
495E VAL* 3.7 20.0 - - + -
440G ASN* 4.8 11.7 - - - -
151H PHE* 4.3 1.6 - + - -
153H TYR* 3.5 54.7 - + - -
155H ARG* 5.4 13.5 - - + +
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Residues in contact with SER 152 (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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143E THR* 3.5 2.1 - - - -
144E ILE* 2.7 47.8 + - - +
146E ILE* 3.8 14.1 - - - -
150E PHE 4.1 0.8 - - - -
151E PHE* 1.3 81.5 - - - +
153E TYR* 1.3 60.6 + - - +
490E THR* 3.7 5.5 - - - +
491E VAL 3.3 3.7 + - - -
492E THR* 2.9 21.0 + - - -
463F SER* 2.8 27.8 + - - -
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Residues in contact with TYR 153 (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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142E LYS 3.1 14.6 - - - +
143E THR* 4.1 9.6 - - + -
144E ILE* 4.5 1.8 - - - +
151E PHE* 3.4 33.4 - + + -
152E SER* 1.3 75.9 + - - +
154E THR* 1.3 71.0 + - - +
155E ARG* 4.0 15.4 - - - -
490E THR* 3.4 3.8 - - - +
491E VAL* 2.9 79.0 + - + +
493E VAL* 4.4 6.1 - - + +
440F ASN* 4.4 7.6 + - - -
443F SER* 3.9 10.6 + - - -
143H THR* 3.8 14.8 - - + -
151H PHE* 3.4 37.8 - + - -
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Residues in contact with THR 154 (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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141E GLY* 3.5 2.5 - - - -
142E LYS* 2.8 28.5 + - - -
144E ILE* 3.8 13.9 - - + -
153E TYR* 1.3 80.4 - - - +
155E ARG* 1.3 58.0 + - - +
156E HIS* 4.2 0.2 + - - -
488E VAL* 3.8 8.1 - - + -
489E LYS 3.1 6.7 - - - -
490E THR* 3.6 22.2 - - - +
464F PRO* 3.7 20.6 - - + -
480F TYR* 2.8 26.4 + - + -
143H THR* 2.8 33.1 + - - +
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Residues in contact with ARG 155 (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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153E TYR* 4.0 25.1 - - + -
154E THR* 1.3 76.7 - - - +
156E HIS* 1.3 64.0 + - - +
157E GLU* 2.6 34.2 + - + +
487E LYS 3.5 2.3 - - - +
488E VAL* 3.6 2.4 - - - -
489E LYS* 2.8 56.4 + - + +
491E VAL* 5.0 3.2 - - - +
443F SER 4.9 0.8 + - - -
444F GLN* 3.3 48.2 + - - +
143H THR* 4.5 9.2 - - - +
151H PHE* 5.3 7.2 - - + -
498H LYS* 6.1 0.4 - - - +
499H ASN 4.1 9.9 + - - -
500H SER* 4.7 6.5 + - - -
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Residues in contact with HIS 156 (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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139E TYR* 3.3 54.0 - + + +
140E HIS 2.9 29.7 + - - -
141E GLY* 3.9 8.4 - - - +
142E LYS* 5.8 2.2 - - + -
154E THR* 4.4 1.1 - - - -
155E ARG* 1.3 75.0 - - - +
157E GLU* 1.3 61.9 + - - +
158E PRO* 4.7 0.7 - - - +
185E THR 5.7 0.5 - - - +
486E THR* 4.3 10.2 - - + +
487E LYS 3.6 4.5 - - - -
488E VAL* 3.9 17.7 - - + +
480F TYR* 2.8 37.3 + + - -
500H SER* 4.3 5.4 - - - +
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Residues in contact with GLU 157 (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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77E ARG* 5.7 3.6 + - - +
155E ARG* 2.6 45.1 + - + +
156E HIS* 1.3 76.8 - - - +
158E PRO* 1.4 74.4 - - + +
185E THR 5.0 0.2 - - - -
486E THR* 3.1 7.0 - - - -
487E LYS* 2.6 52.2 + - + +
489E LYS* 3.0 35.6 + - - +
444F GLN 4.5 0.6 - - - +
447F GLN* 6.0 1.2 - - - -
500H SER* 3.9 14.1 - - - +
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Residues in contact with PRO 158 (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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70E PHE* 3.7 21.4 - - + -
77E ARG* 4.7 1.3 - - - +
156E HIS 4.7 0.4 - - - +
157E GLU* 1.4 90.7 - - + +
159E VAL* 1.3 63.7 + - - +
185E THR 3.2 24.2 - - - +
186E GLY 3.5 18.8 - - - +
187E ASN* 3.6 9.9 - - - +
485E TYR 3.8 7.9 - - - +
486E THR* 5.1 0.2 - - + -
487E LYS* 3.7 10.4 - - - +
500H SER* 3.5 40.4 - - - +
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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