Contacts of the strand formed by residues 195 - 201 (chain E) in PDB entry 1R9T
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 VAL 195 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155E ARG* 5.3 0.4 - - - -
156E LEU* 3.2 50.4 + - + +
161E LYS* 3.2 26.5 - - + +
164E LEU* 4.8 9.2 - - + -
165E LEU* 5.9 2.9 - - + -
175E LEU* 4.9 4.3 - - + -
190E LEU* 5.0 0.7 - - - -
193E GLY 3.8 0.2 + - - -
194E GLU* 1.3 78.5 - - - +
196E VAL* 1.3 83.3 - - - +
211E TYR* 4.2 13.2 - - + -
212E ARG 3.4 9.4 - - - +
213E ILE* 2.9 31.0 - - + -
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Residues in contact with VAL 196 (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 HIS* 4.0 18.6 - - + -
154E ILE 3.6 25.6 - - - +
155E ARG* 4.1 4.9 - - - -
178E ILE* 4.7 11.9 - - + -
188E LEU* 4.7 6.7 - - + -
190E LEU* 4.2 20.9 - - + +
194E GLU 3.6 2.2 + - - -
195E VAL* 1.3 87.9 - - - +
197E LYS* 1.3 60.9 + - - +
198E ILE* 3.6 23.8 - - + -
211E TYR* 3.3 1.9 - - - -
212E ARG* 2.4 56.8 + - + +
213E ILE* 4.3 0.4 - - - +
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Residues in contact with LYS 197 (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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1006A ILE* 5.7 5.4 - - - +
1009A ASN* 5.8 6.1 - - - +
1013A ASP* 5.6 3.2 + - - -
154E ILE* 3.0 43.6 + - + +
156E LEU* 3.0 25.8 - - + -
196E VAL* 1.3 73.7 - - - +
198E ILE* 1.3 68.8 + - - +
199E ILE* 4.4 21.7 - - + +
209E ALA* 4.8 9.0 - - + +
210E SER 3.4 9.2 - - - +
211E TYR* 3.9 36.6 - - + +
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Residues in contact with ILE 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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1342A GLU* 4.6 10.8 - - - +
151E PRO* 4.4 12.3 - - + -
152E LYS 3.6 5.6 - - - +
153E HIS* 3.8 32.1 - - + +
196E VAL* 3.6 17.0 - - + -
197E LYS* 1.3 92.9 - - - +
199E ILE* 1.3 69.1 + - - +
200E ARG* 3.9 2.8 + - + +
208E TYR 3.5 0.9 - - - +
209E ALA 3.4 0.2 - - - -
210E SER* 2.5 49.5 + - - +
212E ARG* 3.5 47.8 - - + +
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Residues in contact with ILE 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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151E PRO* 4.1 9.2 - - - +
152E LYS* 3.2 51.2 + - + +
154E ILE* 4.9 13.9 - - + -
197E LYS* 4.4 26.9 - - + +
198E ILE* 1.3 89.2 - - - +
200E ARG* 1.3 62.6 - - - +
201E LYS* 4.3 6.1 + - + +
207E ARG* 5.7 12.1 - - + +
208E TYR 3.3 8.1 - - - +
209E ALA* 4.9 4.7 - - + -
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Residues in contact with ARG 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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870A GLU* 3.0 30.0 + - - +
1342A GLU* 3.0 41.6 + - - -
1345A ARG* 3.1 30.2 - - - +
1373A ASP* 3.7 20.6 + - - -
151E PRO* 4.3 16.2 - - + -
198E ILE* 3.9 3.2 + - + +
199E ILE* 1.3 76.2 - - - +
201E LYS* 1.3 78.2 - - - +
207E ARG* 3.7 2.5 - - - -
208E TYR* 2.8 61.5 + - + +
210E SER* 4.2 9.4 + - - +
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Residues in contact with LYS 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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870A GLU* 4.2 0.7 - - - +
942A PHE* 5.2 13.6 - - + -
945A GLU* 3.3 43.3 + - + +
946A VAL* 3.4 31.2 - - + +
1345A ARG* 5.5 1.4 + - - -
1365A TYR* 5.5 0.7 + - - -
151E PRO* 5.2 2.6 - - - +
152E LYS* 3.5 29.7 - - - +
199E ILE* 5.3 5.4 - - + -
200E ARG* 1.3 93.4 - - - +
202E SER* 1.4 62.1 + - - +
206E GLY 3.5 13.2 - - - +
207E ARG* 5.3 12.1 - - + +
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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