Contacts of the strand formed by residues 191 - 197 (chain D) in PDB entry 6IAP
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 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D LYS 5.5 0.2 - - - +
150D VAL* 3.6 3.6 - - - +
151D ASP* 2.3 83.8 + - + +
152D ASN 5.4 1.8 - - - +
190D LYS* 1.4 76.7 - - + +
192D TYR* 1.3 63.8 + - - +
193D ALA* 4.2 4.9 - - + +
208D SER* 4.5 15.3 - - - +
209D PHE 3.5 7.6 - - - +
210D ASN* 3.9 15.0 - - - +
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Residues in contact with TYR 192 (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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117D ILE* 3.8 2.8 - - - +
132D VAL* 4.4 5.4 - - + -
148D TRP* 4.7 3.4 - - + -
149D LYS 4.1 2.7 - - - -
150D VAL* 3.2 26.1 - - + +
179D LEU* 4.1 17.3 - - + -
181D LEU* 4.4 16.4 - - + -
185D ASP 3.6 3.3 + - - -
186D TYR* 2.6 61.0 + + - -
189D HIS* 3.3 33.8 + - - +
190D LYS 3.4 13.0 - - - -
191D VAL* 1.3 72.2 - - - +
193D ALA* 1.3 59.3 + - - +
208D SER* 3.3 2.6 - - - -
209D PHE* 3.0 61.8 + + + -
211D ARG* 4.8 1.3 - - + -
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Residues in contact with ALA 193 (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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117D ILE* 4.3 0.7 - - - -
147D GLN 3.9 0.2 - - - +
148D TRP* 3.1 12.3 - - - -
149D LYS* 3.0 42.9 + - + +
191D VAL* 5.0 4.9 - - + -
192D TYR* 1.3 70.8 - - - +
194D CYS* 1.3 59.9 + - - +
195D GLU 4.2 0.4 + - - -
206D THR* 4.0 18.4 - - + -
207D LYS 3.3 5.8 - - - +
208D SER* 3.3 24.5 - - - -
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Residues in contact with CYS 194 (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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115D VAL* 4.1 11.0 - - - -
117D ILE* 3.9 14.1 - - - -
134D CYS* 2.0 54.1 - - + -
146D VAL* 3.8 6.5 - - + -
147D GLN 3.2 8.5 - - - +
148D TRP* 3.7 12.3 - - + -
193D ALA* 1.3 72.0 - - - +
195D GLU* 1.3 60.0 + - - +
196D VAL* 3.9 2.1 + - - +
205D VAL 3.6 2.1 - - - +
206D THR* 4.5 1.8 - - - -
207D LYS* 2.9 34.7 + - - +
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Residues in contact with GLU 195 (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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145D LYS 3.5 2.4 - - - +
146D VAL* 3.3 2.8 - - - -
147D GLN* 2.8 57.9 + - + +
149D LYS* 3.8 32.7 + - + -
154D LEU* 6.1 0.2 - - - +
193D ALA 4.2 1.0 - - - -
194D CYS* 1.3 70.5 - - - +
196D VAL* 1.3 62.0 + - - +
197D THR* 5.0 1.0 + - + -
204D PRO* 4.3 18.6 - - + +
205D VAL 3.3 4.0 - - - +
206D THR* 3.3 29.7 + - + +
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Residues in contact with VAL 196 (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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113D PRO* 4.0 10.1 - - + -
115D VAL* 3.9 24.7 - - + -
134D CYS* 4.4 2.0 - - - -
136D LEU* 3.6 48.5 - - + -
145D LYS 3.6 3.1 - - - +
146D VAL* 4.1 11.0 - - + -
194D CYS 4.6 0.9 - - - +
195D GLU* 1.3 74.8 - - - +
197D THR* 1.3 68.5 + - - +
198D HIS* 4.8 0.2 - - + -
201D LEU* 3.8 21.3 - - + +
204D PRO* 3.1 7.7 - - - +
205D VAL* 2.8 36.5 + - + +
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Residues in contact with THR 197 (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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144D ALA* 3.5 5.7 - - - +
145D LYS* 2.8 61.2 + - - +
195D GLU* 5.0 0.8 + - + -
196D VAL* 1.3 71.1 - - - +
198D HIS* 1.3 62.7 + - - +
201D LEU* 4.8 0.9 - - - -
204D PRO* 3.6 34.1 - - + -
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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