Contacts of the strand formed by residues 198 - 203 (chain D) in PDB entry 3K9X
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 PRO 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D TRP* 4.3 14.4 - - + +
30D GLN* 3.3 25.6 - - - +
44D GLY 3.6 11.7 - - - +
45D THR* 3.3 24.9 - - + +
137D ILE 3.8 0.3 - - - +
138D VAL* 3.4 9.1 - - - +
139D SER* 3.3 39.8 + - - +
197D GLY* 1.4 84.9 - - - +
199D HIS* 1.3 58.7 - - - +
200D VAL* 4.1 20.2 - - + +
209D VAL* 5.8 0.9 - - + -
211D GLY 4.1 2.2 - - - +
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Residues in contact with HIS 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY* 3.8 17.2 + - - -
137D ILE 3.3 9.9 - - - -
138D VAL* 4.7 0.2 - - + -
160D VAL* 3.9 27.4 - - + +
162D TYR* 3.5 25.0 - + - -
181D PHE* 3.8 17.6 - + - -
183D ALA* 4.2 3.4 - - - +
198D PRO* 1.3 72.8 - - - +
200D VAL* 1.3 62.0 + - - +
209D VAL* 3.8 1.6 - - - +
210D THR* 2.8 50.4 + - - -
211D GLY* 3.0 28.7 + - - +
228D TYR* 3.7 41.7 - + + -
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TRP* 4.0 26.5 - - + +
121D ALA* 4.3 12.8 - - + -
136D GLY* 3.2 3.5 - - - -
137D ILE* 2.9 51.2 + - + +
198D PRO* 4.2 13.5 - - + -
199D HIS* 1.3 79.9 + - - +
201D THR* 1.3 64.4 + - - +
202D ARG 4.3 0.2 - - - -
207D TYR* 3.7 27.8 - - + -
208D PHE 3.2 18.6 - - - +
209D VAL* 4.2 5.6 - - + +
210D THR* 3.4 1.6 - - - -
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Residues in contact with THR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.7 28.3 - - + +
133D GLN* 3.9 20.4 - - + +
135D THR 3.9 14.8 - - - +
136D GLY* 4.0 3.7 - - - -
137D ILE* 5.2 0.2 - - - -
162D TYR* 2.6 27.1 + - - +
199D HIS* 3.9 1.2 - - - -
200D VAL* 1.3 74.3 + - - +
202D ARG* 1.3 61.6 + - - +
206D THR 3.8 1.2 - - - +
207D TYR* 3.7 2.6 - - - -
208D PHE* 2.9 35.0 + - - +
210D THR* 2.8 22.1 + - - -
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Residues in contact with ARG 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C GLN* 4.6 7.7 + - - +
133D GLN* 3.0 24.6 + - - +
135D THR 5.3 1.0 + - - -
137D ILE* 4.9 6.5 - - + +
201D THR* 1.3 72.5 - - - +
203D PHE* 1.3 61.9 + - - +
204D LYS 4.8 0.4 - - - +
205D ASP* 2.3 56.5 + - - +
206D THR 3.5 7.2 - - - +
207D TYR* 2.8 57.6 + - + -
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Residues in contact with PHE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ASN* 3.5 43.3 - - + -
137C ASP 4.3 7.3 - - - +
138C GLN* 5.1 0.2 - - - -
127D TRP* 3.6 17.0 - + - -
131D LEU* 3.6 35.9 - - + -
133D GLN* 3.6 19.5 - - - -
201D THR 3.8 0.4 + - - -
202D ARG* 1.3 73.9 - - - +
204D LYS* 1.3 96.9 + - + +
205D ASP 3.3 0.7 - - - -
206D THR* 2.9 23.6 + - - +
208D PHE* 4.1 8.8 - + + -
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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