Contacts of the strand formed by residues 195 - 201 (chain M) in PDB entry 1I9R
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153M LYS 3.7 2.4 - - - +
154M VAL* 3.5 1.7 - - - +
155M ASP* 2.5 47.7 + - - +
156M ASN* 4.5 13.5 - - - +
194M LYS* 1.3 81.8 - - + +
196M TYR* 1.3 65.5 + - - +
197M ALA* 5.1 6.1 - - + -
212M SER* 5.1 5.4 - - - -
213M PHE 3.4 5.6 - - - +
214M ASN* 3.0 29.8 - - - +
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Residues in contact with TYR 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M ILE* 4.0 2.5 - - - +
136M VAL* 4.8 3.4 - - + -
152M TRP* 4.9 7.4 - + + -
153M LYS 3.7 2.5 - - - -
154M VAL* 3.2 24.7 - - + -
183M LEU* 4.2 10.1 - - + -
185M LEU* 3.2 25.9 - - + +
189M ASP 3.2 6.8 + - - -
190M TYR* 2.6 65.7 + + - -
193M HIS* 3.3 20.8 - - + +
194M LYS 4.1 6.1 - - - -
195M VAL* 1.3 72.8 - - - +
197M ALA* 1.3 63.0 + - - +
212M SER* 3.3 1.4 - - - -
213M PHE* 3.1 53.6 + + + +
215M ARG* 3.8 15.5 - - + -
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Residues in contact with ALA 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M ILE* 4.5 1.1 - - - -
151M GLN 3.9 0.2 - - - +
152M TRP* 3.5 8.5 - - - -
153M LYS* 2.7 53.5 + - + +
195M VAL* 5.1 5.6 - - + -
196M TYR* 1.3 75.2 - - - +
198M CYS* 1.3 62.0 + - - +
199M GLU* 3.8 1.4 + - - +
210M THR* 4.2 13.7 - - + -
211M LYS 3.5 4.5 - - - +
212M SER* 3.2 25.1 - - - -
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Residues in contact with CYS 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M VAL* 5.0 1.8 - - - -
121M ILE* 4.2 3.3 - - + +
138M CYS* 2.1 55.4 - - + -
150M VAL* 4.5 6.1 - - + -
151M GLN 3.5 6.5 - - - +
152M TRP* 3.9 20.9 - - + +
197M ALA* 1.3 74.0 - - - +
199M GLU* 1.3 59.0 + - - +
200M VAL* 4.2 7.8 + - - +
209M VAL 4.3 0.3 - - - +
210M THR* 3.8 0.4 - - - -
211M LYS* 3.0 39.7 + - - +
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Residues in contact with GLU 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149M LYS 3.9 0.7 - - - +
150M VAL* 3.3 2.8 - - - -
151M GLN* 2.8 64.4 + - - +
153M LYS* 3.2 38.5 + - - +
197M ALA 3.8 1.0 + - - +
198M CYS* 1.3 73.6 - - - +
200M VAL* 1.3 59.6 + - - +
201M THR* 4.2 4.9 + - - +
208M PRO* 4.0 23.4 - - + +
209M VAL 3.7 7.0 - - - +
210M THR* 3.4 21.2 + - + +
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Residues in contact with VAL 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M PRO* 4.2 6.3 - - + -
119M VAL* 3.3 34.5 - - + -
140M LEU* 3.5 31.6 - - + -
149M LYS 3.1 8.1 - - - +
150M VAL* 4.2 5.4 - - + +
198M CYS* 4.9 4.7 - - - +
199M GLU* 1.3 74.8 - - - +
201M THR* 1.3 70.6 + - - +
202M HIS* 4.4 1.1 - - + -
205M LEU* 3.6 18.0 - - + +
208M PRO* 3.5 4.2 - - - +
209M VAL* 3.1 37.9 + - + +
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Residues in contact with THR 201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148M ALA 3.6 0.5 - - - -
149M LYS* 2.8 67.0 + - - +
199M GLU* 4.6 4.0 + - - +
200M VAL* 1.3 75.6 - - - +
202M HIS* 1.3 66.5 + - - +
208M PRO* 3.5 33.4 - - + +
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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