Contacts of the strand formed by residues 197 - 202 (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 SER 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E MET* 3.3 19.2 - - - +
40E HIS* 5.7 0.2 - - - -
43E GLY* 3.5 10.9 - - - -
44E ALA 4.4 0.2 - - - +
139E MET 3.0 26.6 + - - -
140E GLY* 4.0 1.6 - - - -
193E GLY 4.5 0.3 + - - -
194E ASP* 2.9 24.1 + - - -
195E SER 3.0 1.6 + - - -
196E GLY* 1.4 76.7 - - - +
198E PRO* 1.3 72.1 - - - +
212E ILE* 3.6 1.4 - - - -
213E ALA* 2.9 27.4 + - - +
228E PHE* 4.3 0.7 - - - -
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Residues in contact with PRO 198 (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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29E PHE* 3.9 22.9 - - + -
30E MET* 3.5 18.2 - - - -
44E ALA 4.5 0.7 - - - +
45E THR* 3.3 25.5 - - - +
137E LEU 4.1 0.9 - - - +
138E ALA* 3.9 3.5 - - - +
139E MET* 3.8 33.7 + - + +
196E GLY 4.4 0.2 - - - +
197E SER* 1.3 91.7 - - - +
199E LEU* 1.3 60.1 - - - +
200E VAL* 4.0 2.2 - - + -
209E ILE* 3.7 25.4 - - + -
211E GLY 3.4 6.5 - - - +
212E ILE* 4.9 0.7 - - + -
228E PHE* 4.7 1.8 - - - -
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Residues in contact with LEU 199 (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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136E CYS* 3.7 11.0 - - + -
137E LEU 3.7 9.0 - - - +
138E ALA* 4.4 1.1 - - + -
160E VAL* 3.6 31.2 - - + -
181E VAL* 3.9 26.7 - - + -
183E THR* 4.0 14.4 - - + -
198E PRO* 1.3 74.5 - - - +
200E VAL* 1.3 61.2 + - - +
201E CYS* 3.9 20.1 + - - -
209E ILE* 3.7 3.1 - - - -
210E HIS* 2.9 25.7 + - + -
211E GLY* 3.0 24.1 + - - +
228E PHE* 3.6 26.7 - - + -
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Residues in contact with VAL 200 (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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8A FUC 3.2 38.8 - - + +
27E TRP* 5.0 3.6 - - + -
29E PHE* 4.4 8.1 - - + -
136E CYS* 3.2 2.6 - - - +
137E LEU* 3.0 32.9 + - + +
139E MET* 3.6 30.5 - - + -
198E PRO* 4.4 4.3 - - + -
199E LEU* 1.3 77.9 - - - +
201E CYS* 1.3 62.0 + - - +
207E GLY* 4.4 10.8 - - - +
208E LEU 3.4 9.0 - - - +
209E ILE* 4.1 19.1 - - + -
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Residues in contact with CYS 201 (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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8A FUC 3.5 5.4 - - - +
130E LEU* 3.5 29.4 - - + -
134E VAL* 4.5 5.2 - - + -
136E CYS* 2.0 45.1 - - - -
199E LEU* 3.9 15.7 - - - -
200E VAL* 1.3 74.9 - - - +
202E ASN* 1.3 67.0 + - - +
207E GLY 3.2 0.2 - - - -
208E LEU* 2.9 25.2 + - - +
210E HIS* 3.5 23.9 + - + -
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Residues in contact with ASN 202 (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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8A FUC 2.9 22.8 + - - -
130E LEU* 4.9 6.1 - - - +
134E VAL* 4.2 19.5 - - - +
135E GLN 5.0 1.7 - - - +
201E CYS* 1.3 73.7 + - - +
207E GLY* 1.3 58.6 + - - +
208E LEU* 3.2 22.3 + - + +
210E HIS* 5.7 0.6 + - - -
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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