Contacts of the strand formed by residues 133 - 146 (chain E) in PDB entry 1PPF
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 ASN* 1.3 75.5 + - - +
134E VAL* 1.3 68.4 + - - +
135E GLN* 3.4 14.9 + - - +
161E THR* 3.6 11.0 - - - -
162E VAL 2.8 17.3 + - - -
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Residues in contact with VAL 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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130E LEU* 4.1 22.7 - - + -
131E GLY 2.9 34.6 + - - +
132E ASN 4.8 0.7 - - - +
133E GLY* 1.3 77.0 - - - +
135E GLN* 1.3 70.1 + - - +
136E CYS* 3.7 9.3 + - - -
161E THR* 3.4 4.9 - - - -
162E VAL* 2.9 40.0 + - + +
201E CYS* 4.5 0.4 - - + -
202E ASN* 4.2 16.6 - - - +
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Residues in contact with GLN 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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1A NAG 3.6 24.4 + - - +
8A FUC 2.7 37.1 + - - +
133E GLY 3.4 14.3 + - - +
134E VAL* 1.3 78.3 - - - +
136E CYS* 1.3 56.0 + - - +
159E ASN* 4.8 9.9 - - - +
160E VAL 3.8 7.2 + - - -
161E THR* 2.7 28.7 + - - +
202E ASN* 4.8 2.3 + - - +
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Residues in contact with CYS 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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1A NAG 5.3 1.3 - - - -
8A FUC 3.8 4.9 - - - -
134E VAL* 4.0 3.4 - - - -
135E GLN* 1.3 77.0 - - - +
137E LEU* 1.3 62.0 + - - +
159E ASN* 3.5 9.3 + - - +
160E VAL* 2.8 35.0 + - + +
162E VAL* 3.7 23.6 - - - -
199E LEU* 3.7 15.5 - - + -
200E VAL 3.2 8.3 - - - +
201E CYS* 2.0 49.8 - - - -
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Residues in contact with LEU 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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1A NAG 4.0 16.8 - - - +
8A FUC 4.1 14.8 - - + -
20E ARG* 3.8 11.9 - - - +
27E TRP* 3.2 43.1 - - + +
136E CYS* 1.3 77.3 - - - +
138E ALA* 1.3 68.7 + - - +
139E MET* 4.3 6.3 - - + +
157E GLU* 4.1 12.1 - - + +
158E LEU 3.4 20.2 - - - +
159E ASN* 3.7 24.2 - - - +
198E PRO 4.1 0.2 - - - +
199E LEU* 3.7 5.6 - - - -
200E VAL* 3.0 34.8 + - + +
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Residues in contact with ALA 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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16E ILE* 4.6 1.6 - - + -
136E CYS 4.3 0.2 + - - -
137E LEU* 1.3 76.0 - - - +
139E MET* 1.3 67.6 + - - +
157E GLU* 3.1 3.9 - - - +
158E LEU* 2.7 42.9 + - + +
160E VAL* 4.3 16.3 - - + +
190E VAL* 4.5 12.1 - - + -
198E PRO 3.9 6.3 - - - +
199E LEU* 4.4 11.0 - - + -
228E PHE* 4.4 15.7 - - + -
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Residues in contact with MET 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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16E ILE* 3.7 12.7 - - - +
27E TRP* 3.7 50.7 - - + +
29E PHE* 4.2 1.8 - - + -
30E MET* 4.1 19.1 - - - +
137E LEU* 4.3 11.9 - - + +
138E ALA* 1.3 83.0 - - - +
140E GLY* 1.3 60.7 + - - +
155E LEU* 4.5 4.7 - - + -
156E GLN 3.1 15.5 - - - +
157E GLU* 4.1 4.5 - - + -
190E VAL* 5.8 0.9 - - - +
194E ASP* 4.3 0.9 - - - +
197E SER* 3.0 23.9 - - - -
198E PRO* 3.8 25.0 + - + +
200E VAL* 3.6 30.1 - - + -
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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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16E ILE* 3.7 3.3 - - - +
30E MET* 3.9 10.1 - - - -
139E MET* 1.3 77.0 - - - +
141E TRP* 1.3 59.6 + - - -
155E LEU* 3.5 14.9 - - - +
156E GLN* 3.1 35.2 + - - +
194E ASP* 2.9 18.1 - - - +
197E SER* 4.0 3.4 - - - -
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Residues in contact with TRP 141 (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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30E MET* 3.9 37.0 - - + +
31E VAL 3.8 13.7 - - - -
32E SER* 3.5 21.3 - - - -
40E HIS* 3.8 29.5 + + + +
70E ALA* 3.9 37.5 - - + -
71E HIS 3.1 27.7 + - - -
73E LEU* 3.6 23.5 - - + +
140E GLY* 1.3 73.1 - - - -
142E GLY* 1.3 64.2 + - - +
151E ILE* 3.2 19.5 - - - +
152E ALA* 3.5 14.5 + - - +
153E SER 3.4 22.1 + - - -
154E VAL 3.9 0.7 - - - -
155E LEU* 3.1 28.6 - - + +
193E GLY 4.3 5.9 + - - -
194E ASP* 3.2 0.6 + - - -
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Residues in contact with GLY 142 (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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16E ILE 3.3 8.7 + - - +
140E GLY 3.4 1.2 + - - +
141E TRP* 1.3 76.6 - - - +
143E LEU* 1.3 68.4 + - - +
144E LEU* 3.6 1.2 + - - +
151E ILE* 4.1 4.7 - - - -
152E ALA* 3.4 15.9 + - - +
192E PHE 3.2 14.6 - - - -
193E GLY* 3.6 11.2 + - - -
194E ASP* 2.7 25.0 + - - -
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Residues in contact with LEU 143 (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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16E ILE 3.0 22.6 + - - +
17E VAL* 3.8 0.2 - - - +
142E GLY* 1.3 71.9 - - - -
144E LEU* 1.3 59.5 + - - +
145E GLY 3.1 24.9 + - - +
146E ARG* 5.0 1.8 - - - -
147E ASN* 4.7 13.2 - - - +
150E GLY* 3.4 11.2 - - - +
151E ILE* 3.5 31.2 - - + +
191E CYS* 3.7 27.0 - - - +
192E PHE* 2.9 35.5 + - + +
20I TYR* 3.9 17.9 - - + +
30I THR* 5.6 1.3 - - + +
32I GLY* 4.9 8.3 - - - +
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Residues in contact with LEU 144 (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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16E ILE 3.5 17.9 - - - +
17E VAL* 3.8 13.1 - - - +
18E GLY 4.6 1.6 + - - -
142E GLY 3.9 2.5 - - - +
143E LEU* 1.3 73.2 - - - +
145E GLY* 1.3 58.2 + - - +
148E ARG* 3.3 37.2 + - + +
150E GLY 2.7 21.4 + - - +
151E ILE 4.5 2.2 - - - +
152E ALA* 3.5 36.3 - - + -
156E GLN* 3.8 23.1 - - + +
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Residues in contact with GLY 145 (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 VAL* 3.6 17.1 - - - +
143E LEU* 3.1 21.4 + - - +
144E LEU* 1.3 85.4 - - - +
146E ARG* 1.3 65.3 + - - -
147E ASN 2.8 10.0 + - - -
148E ARG* 3.1 23.1 + - - -
191E CYS* 5.2 1.8 - - - -
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Residues in contact with ARG 146 (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 VAL* 5.0 0.8 - - - +
143E LEU* 5.0 4.0 - - - -
145E GLY* 1.3 67.6 - - - -
147E ASN* 1.3 84.3 + - - +
148E ARG* 4.3 23.6 - - - +
187E GLN* 5.9 2.4 - - - +
191E CYS* 5.4 3.4 - - - -
220E CYS* 5.9 6.6 - - + +
29I LYS* 5.7 5.4 - - - +
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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