Contacts of the strand formed by residues 197 - 202 (chain D) in PDB entry 6Q3W
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 HIS 197 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D MET* 4.4 10.9 - - - +
56D ALA 5.1 2.6 + - - -
189D ILE* 6.0 0.3 - - - +
194D GLN* 3.1 46.3 + - + +
195D LYS 2.7 26.7 + - - -
196D GLY* 1.3 81.7 - - - +
198D ALA* 1.3 61.9 + - - +
210D LEU* 4.1 32.1 - - + -
211D VAL 3.3 6.7 - - - +
212D PRO* 3.6 34.9 - - + +
213D LEU* 4.1 9.2 - - - +
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 4.2 17.3 - - + -
53D LEU* 3.9 19.7 - - + -
54D PRO 3.7 9.4 - - - +
55D MET* 4.5 3.1 - - + +
189D ILE* 5.9 0.2 - - - -
197D HIS* 1.3 74.9 - - - +
199D LEU* 1.3 61.9 + - - +
200D LEU 4.0 0.4 - - - -
209D SER 3.5 0.9 - - - +
210D LEU* 3.5 5.1 - - - +
211D VAL* 2.8 36.6 + - + +
213D LEU* 4.1 11.3 - - + +
295D LEU* 4.3 11.0 - - + -
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D VAL 3.4 0.2 - - - +
53D LEU* 3.5 3.3 - - - -
54D PRO* 2.9 44.3 + - + +
188D PHE 4.3 1.8 - - - +
189D ILE* 4.0 28.9 - - + +
192D MET* 3.9 32.8 - - + -
193D GLY* 5.9 0.7 - - - -
198D ALA* 1.3 72.8 - - - +
200D LEU* 1.3 62.1 + - - +
201D ILE* 3.4 27.4 + - + -
208D THR* 3.8 21.1 - - - +
209D SER 3.4 16.6 - - - +
210D LEU* 3.9 20.9 - - + -
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 4.4 18.2 - - + -
52D VAL 3.6 13.5 - - - +
53D LEU* 3.7 13.4 - - + +
198D ALA 3.9 1.0 + - - -
199D LEU* 1.3 71.0 - - - +
201D ILE* 1.3 62.8 + - - +
202D ASP* 4.9 2.9 - - + +
207D GLU 3.8 1.0 - - - +
208D THR* 3.2 6.4 - - - -
209D SER* 2.9 45.9 + - - +
211D VAL* 4.6 6.9 - - + +
288D THR* 4.2 21.3 - - + +
289D ALA* 5.8 1.6 - - - -
292D ALA* 4.1 18.8 - - + -
296D ARG* 3.9 23.3 - - - +
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Residues in contact with ILE 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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51D LEU* 3.5 2.7 - - - -
52D VAL* 2.9 43.8 + - + +
54D PRO* 4.1 11.4 - - + -
185D MET* 3.5 42.0 - - + +
188D PHE* 4.4 13.2 - - + -
189D ILE 5.0 0.2 - - - +
199D LEU* 3.8 31.9 - - + +
200D LEU* 1.3 78.2 - - - +
202D ASP* 1.3 70.0 + - - +
203D CYS* 3.4 5.7 + - - -
206D LEU* 5.7 4.0 - - + -
207D GLU 3.9 2.2 - - - -
208D THR* 3.9 17.5 - - + -
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Residues in contact with ASP 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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51D LEU* 3.6 14.5 - - + +
200D LEU* 4.0 4.6 + - + +
201D ILE* 1.3 72.3 - - - +
203D CYS* 1.3 57.7 + - - +
204D ARG* 2.6 31.6 + - - +
205D SER* 3.3 26.9 + - - +
206D LEU* 2.9 32.4 + - - +
207D GLU* 3.1 18.4 + - + +
256D ARG* 2.9 35.7 + - - -
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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