Contacts of the strand formed by residues 133 - 140 (chain E) in PDB entry 2SGD
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 GLY 133 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E VAL* 1.3 75.7 - - - +
134E MET* 1.3 66.5 + - - +
135E ALA* 3.4 2.3 + - - +
161E SER* 4.7 7.8 + - - -
162E VAL 2.8 17.8 + - - -
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Residues in contact with MET 134 (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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128E ALA* 5.7 0.7 - - + -
129E ASN 3.7 19.3 - - - +
130E ALA* 4.3 8.3 - - - -
131E THR* 2.9 38.4 + - + +
132E VAL 3.3 1.2 + - - -
133E GLY* 1.3 78.0 - - - +
135E ALA* 1.3 72.7 + - - +
136E VAL* 3.6 17.7 + - + -
161E SER* 3.1 6.2 - - - -
162E VAL* 3.0 29.2 + - + +
201E SER* 4.0 8.5 - - - +
208E ARG* 3.9 28.3 - - - +
210E ILE* 3.9 22.4 - - + -
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Residues in contact with ALA 135 (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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133E GLY 3.4 2.5 + - - +
134E MET* 1.3 74.0 - - - +
136E VAL* 1.3 61.9 + - - +
137E THR* 5.4 0.4 - - - -
160E GLY 3.5 9.0 - - - +
161E SER* 4.5 4.7 - - - +
201E SER* 2.9 25.8 + - - -
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Residues in contact with VAL 136 (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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134E MET* 3.6 26.5 - - + -
135E ALA* 1.3 80.0 - - - +
137E THR* 1.3 65.8 + - - +
159E SER* 3.3 4.0 - - - -
160E GLY 2.9 38.3 + - - +
161E SER 4.5 4.7 - - - -
162E VAL* 4.0 11.2 - - + -
183E THR* 4.3 10.3 - - + -
190E VAL* 4.1 11.2 - - + -
199E LEU* 3.2 37.2 - - + -
200E TYR 3.2 13.7 - - - +
201E SER* 4.4 1.3 - - - +
210E ILE* 4.5 4.0 - - + -
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Residues in contact with THR 137 (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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135E ALA 5.4 0.3 - - - -
136E VAL* 1.3 78.7 + - - +
138E ARG* 1.4 62.3 + - - +
157E THR* 3.5 25.6 - - + -
158E HIS 3.5 5.2 - - - -
159E SER* 3.5 15.4 + - - +
190E VAL* 5.5 0.4 - - - -
199E LEU* 3.4 5.8 - - - +
200E TYR* 2.8 71.1 + - + +
201E SER* 5.3 2.4 - - - -
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Residues in contact with ARG 138 (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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137E THR* 1.4 74.8 - - - +
139E ARG* 1.3 75.7 + - - +
140E GLY* 3.1 33.9 - - - +
143E THR* 2.7 29.4 + - - -
156E GLY 3.3 6.2 + - - +
157E THR* 3.1 7.3 - - - +
158E HIS* 2.9 54.1 + - - +
190E VAL* 3.9 14.1 - - + -
191E CYS 2.7 30.9 + - - -
192E ALA* 3.7 11.7 - - - +
194E ASP* 3.6 9.6 + - - -
198E PRO 3.3 10.1 - - - +
199E LEU* 4.2 7.6 - - + +
200E TYR* 4.7 0.4 - - - -
213E THR* 3.5 26.7 - - - +
220E CYS* 4.1 0.4 - - - -
228E PHE* 3.9 16.2 - - + -
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Residues in contact with ARG 139 (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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17E SER* 4.2 1.2 + - - -
18E GLY 2.8 33.7 + - - -
19E GLY* 3.4 6.3 + - - -
29E ASP* 3.0 36.0 + - - +
119E VAL* 3.7 25.6 - - + -
120E GLY* 3.8 22.6 - - - +
138E ARG* 1.3 83.0 + - - +
140E GLY* 1.3 63.3 + - - +
156E GLY* 3.5 9.9 - - - +
157E THR* 3.9 19.0 + - - +
197E GLY* 3.4 9.9 - - - -
198E PRO* 3.2 27.7 + - + +
200E TYR* 4.6 3.8 - - + +
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Residues in contact with GLY 140 (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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19E GLY 3.5 7.1 - - - +
43E SER* 3.8 6.7 - - - -
138E ARG* 3.1 9.6 - - - +
139E ARG* 1.3 80.6 - - - +
141E SER* 1.3 63.5 + - - -
156E GLY* 3.0 27.0 + - - -
194E ASP* 3.2 21.3 - - - -
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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