Contacts of the strand formed by residues 149 - 155 (chain E) in PDB entry 3ZWG
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 TRP 149 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148E GLY* 1.3 71.6 - - - -
150E HIS* 1.3 60.8 + - - +
151E SER* 4.5 1.7 + - - +
161E ARG* 3.4 37.7 - - + -
162E GLY* 3.3 42.6 - - - -
163E PHE* 3.5 26.8 - + + -
173E GLU* 3.9 27.8 - - + -
175E HIS* 4.5 1.8 - + - -
47F ALA* 3.6 31.6 - - + +
48F MET* 2.7 18.8 + - - +
60F VAL* 3.3 21.3 - - + -
61F LEU* 3.0 21.2 + - + -
63F HIS* 3.8 23.7 + - + -
127F ARG* 2.9 24.1 + - - -
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Residues in contact with HIS 150 (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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117E TRP* 3.7 14.5 - + + -
143E PHE* 3.2 53.2 - + + +
144E ARG 4.0 5.7 + - - -
146E ASP* 2.8 39.7 + - - -
148E GLY 3.3 19.0 + - - -
149E TRP* 1.3 73.9 + - - +
151E SER* 1.3 63.6 + - - +
160E SER 3.6 1.6 - - - +
161E ARG* 3.5 1.8 - - - -
162E GLY 2.9 31.5 + - - +
127F ARG* 3.2 21.2 + - - -
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Residues in contact with SER 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E PHE* 4.7 3.0 - - - -
149E TRP* 5.4 2.1 - - - +
150E HIS* 1.3 77.0 - - - +
152E ARG* 1.3 62.8 + - - +
159E LYS* 5.3 12.8 - - - -
160E SER 3.1 9.2 - - - -
161E ARG* 3.6 23.1 - - - +
63F HIS* 6.0 0.2 - - - -
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Residues in contact with ARG 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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118E ASN* 3.4 14.6 + - - -
119E VAL 4.1 7.8 + - - -
120E ARG* 2.5 46.8 - - - +
140E ARG 3.8 1.9 + - - -
141E SER* 2.7 29.6 + - - -
143E PHE* 3.4 43.5 - - + -
150E HIS 4.3 0.4 + - - -
151E SER* 1.3 76.4 - - - +
153E GLY* 1.3 77.6 + - - +
154E LEU* 3.6 2.3 + - - +
159E LYS* 4.3 4.2 - - - +
160E SER* 2.9 36.2 + - - +
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Residues in contact with GLY 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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120E ARG* 4.8 3.6 + - - -
152E ARG* 1.3 90.7 - - - +
154E LEU* 1.3 61.0 + - - -
155E GLY 3.5 2.7 - - - -
158E LEU 4.0 1.8 - - - -
159E LYS* 3.9 14.3 - - - +
179E ALA* 6.1 0.2 - - - -
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Residues in contact with LEU 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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100E LEU* 4.1 7.4 - - + -
119E VAL* 3.3 47.1 - - + +
120E ARG* 3.9 15.8 + - - +
121E VAL* 3.6 32.6 + - + +
152E ARG* 4.5 3.4 - - - +
153E GLY* 1.3 75.6 - - - +
155E GLY* 1.3 61.6 + - - +
156E TYR* 3.6 13.0 - - - -
158E LEU* 2.9 23.4 + - + +
159E LYS* 4.1 5.2 - - - -
160E SER* 3.8 34.1 - - - +
176E VAL* 4.3 6.7 - - + -
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Residues in contact with GLY 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 GLY* 3.5 3.0 - - - -
154E LEU* 1.3 82.9 - - - +
156E TYR* 1.3 63.1 + - - +
157E GLY 2.8 17.5 + - - -
158E LEU* 2.8 19.3 + - - +
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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