Contacts of the strand formed by residues 297 - 305 (chain D) in PDB entry 6C3P
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 THR 297 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C ILE* 3.7 34.2 - - + +
290C VAL* 4.2 27.2 - - + +
292C GLU 4.6 8.3 - - - +
295C GLY* 4.4 7.3 + - - -
174D ALA* 4.4 9.2 - - - +
288D GLU* 5.0 1.6 - - + -
289D GLY* 3.1 24.5 - - - +
290D VAL* 3.5 19.0 - - + +
291D VAL* 5.2 0.2 - - - -
295D GLY 4.7 1.0 + - - -
296D ILE* 1.3 78.4 - - - +
298D THR* 1.3 63.9 + - - +
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Residues in contact with THR 298 (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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211C ILE* 4.9 2.7 - - - -
174D ALA* 4.3 13.8 - - - +
175D HIS* 4.0 9.7 + - - +
177D ARG* 5.0 3.1 - - + -
178D ALA* 3.3 30.0 - - + +
181D LEU* 4.9 12.3 - - + -
210D ILE* 4.1 12.6 - - + -
287D LEU 3.9 0.3 - - - +
288D GLU* 3.5 3.5 - - - -
289D GLY 3.0 29.7 + - - +
291D VAL* 4.0 20.2 - - + -
296D ILE 4.2 0.2 + - - -
297D THR* 1.3 79.7 - - - +
299D GLN* 1.3 68.2 + - - +
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Residues in contact with GLN 299 (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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209C MET* 4.1 6.8 - - - +
210C ILE 4.0 9.0 - - - +
211C ILE* 3.5 27.0 - - + +
250C PHE* 3.3 19.8 - - - -
175D HIS* 5.8 0.5 - - - +
178D ALA* 3.8 11.6 - - - +
286D ILE* 3.3 22.6 - - + +
287D LEU 3.2 12.1 - - - +
288D GLU* 3.2 20.6 + - + +
298D THR* 1.3 82.5 + - - +
300D ALA* 1.3 61.8 + - - +
301D ARG* 2.5 53.8 + - - +
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Residues in contact with ALA 300 (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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178D ALA* 3.8 23.1 - - + +
181D LEU* 4.2 21.5 - - + +
183D PHE* 4.1 23.2 - - + -
285D VAL 4.0 0.2 - - - +
286D ILE* 3.9 0.5 - - - -
287D LEU* 3.0 33.0 + - + +
299D GLN* 1.3 74.0 - - - +
301D ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 301 (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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209C MET* 4.9 11.3 - - - +
250C PHE* 3.9 22.2 - - + -
292C GLU* 4.1 20.0 + - - +
36D VAL* 3.9 12.3 - - + -
38D LYS 4.8 0.3 - - - +
39D LYS* 3.9 3.6 - - - -
40D GLY* 3.3 50.7 + - - -
42D CYS* 4.8 10.5 - - - -
183D PHE* 4.8 4.7 - - - -
284D ILE* 5.3 1.8 - - + -
285D VAL 3.6 3.4 - - - +
286D ILE* 4.3 7.4 - - + -
299D GLN* 2.5 71.9 + - - +
300D ALA* 1.3 77.0 - - - +
302D THR* 1.3 64.5 + - - +
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Residues in contact with THR 302 (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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36D VAL* 5.0 2.2 - - - -
37D SER 4.4 6.3 - - - -
38D LYS* 4.0 19.2 + - - -
183D PHE* 3.5 47.2 + - + +
284D ILE* 4.0 1.9 - - - +
285D VAL* 2.8 49.3 + - + +
301D ARG* 1.3 76.5 - - - +
303D SER* 1.3 70.6 + - - +
304D TYR* 4.2 14.5 - - + -
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Residues in contact with SER 303 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D ARG* 2.3 40.6 + - - -
36D VAL* 2.4 26.6 + - - -
37D SER 4.0 3.5 + - - -
38D LYS* 3.2 14.4 - - - +
282D GLU* 3.1 22.4 + - - -
283D ILE 3.8 5.2 - - - -
284D ILE* 3.8 13.5 - - - -
302D THR* 1.3 78.2 + - - +
304D TYR* 1.3 68.5 + - - +
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Residues in contact with TYR 304 (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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38D LYS* 4.0 5.8 - - - -
183D PHE* 3.7 10.2 - - - +
184D SER* 2.1 43.8 + - - -
185D LYS 3.5 18.2 - - - -
186D HIS 3.7 9.6 - - - -
187D ALA* 4.2 14.4 - - + -
198D PHE* 5.1 6.3 - + + -
200D LEU* 3.5 31.8 - - + +
282D GLU* 3.2 4.1 - - - -
283D ILE* 2.9 33.3 + - + +
285D VAL* 4.3 11.0 - - + -
302D THR* 4.2 18.1 + - + -
303D SER* 1.3 75.6 - - - +
305D LEU* 1.3 62.0 + - - +
308D GLU* 3.2 26.5 - - + +
309D ILE* 4.1 22.0 - - + +
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Residues in contact with LEU 305 (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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32D ARG* 3.9 12.8 - - + +
33D ALA 5.7 1.8 - - - +
34D ARG* 3.1 46.7 - - + +
277D HIS* 3.4 44.0 - - + +
281D LEU 3.3 19.1 - - - +
282D GLU* 4.0 8.5 - - + +
304D TYR* 1.3 77.2 - - - +
306D ALA* 1.3 75.3 + - - +
307D ASP* 3.1 30.1 + - - +
308D GLU* 3.4 10.7 + - - -
309D ILE* 3.3 15.2 + - - +
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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