Contacts of the strand formed by residues 297 - 305 (chain E) in PDB entry 5TWV
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289E GLY* 3.1 14.6 - - - +
290E VAL* 3.5 26.9 - - + -
295E GLY 3.6 4.0 + - - +
296E ILE* 1.3 82.5 - - - +
298E THR* 1.3 60.2 + - - +
211G ILE* 4.4 18.5 - - - +
290G VAL* 3.9 26.2 - - - +
291G VAL 5.1 4.2 - - - +
292G GLU* 5.2 4.2 - - - +
295G GLY* 5.7 1.2 - - - -
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Residues in contact with THR 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E ALA* 3.4 28.6 + - + +
175E HIS* 4.3 7.7 + - - -
177E ARG* 5.1 3.4 - - + -
178E ALA* 3.0 37.6 - - + +
181E LEU* 4.9 7.6 - - + -
210E ILE* 5.6 6.3 - - + -
287E LEU 3.9 0.3 - - - +
288E GLU* 3.5 4.7 - - - +
289E GLY* 2.8 36.6 + - - +
290E VAL* 5.8 1.8 - - - -
291E VAL* 6.0 1.3 - - + +
296E ILE 4.0 1.5 + - - +
297E THR* 1.3 73.0 - - - +
299E GLN* 1.3 69.6 + - - +
211G ILE* 4.7 4.2 - - - +
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Residues in contact with GLN 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E HIS* 5.9 1.0 + - - -
178E ALA* 4.2 5.3 - - - +
286E ILE* 3.4 19.6 - - + +
287E LEU 3.2 23.4 - - - +
288E GLU* 3.9 18.6 - - + +
298E THR* 1.3 85.7 + - - +
300E ALA* 1.3 87.7 + - - +
301E ARG* 2.9 53.0 + - - +
209G MET* 5.6 0.7 - - - +
211G ILE* 3.9 28.2 - - + +
250G PHE* 4.1 8.0 - - - -
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Residues in contact with ALA 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E ALA* 4.3 11.0 - - + +
181E LEU* 4.2 27.6 - - + +
183E PHE* 3.8 19.1 - - + -
285E VAL 3.6 1.7 - - - +
287E LEU* 2.9 32.3 + - + +
299E GLN* 1.3 84.6 + - - +
301E ARG* 1.3 59.2 + - - +
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Residues in contact with ARG 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 5.0 6.5 - - + -
39E LYS 3.2 4.2 + - - +
40E GLY* 3.2 31.4 - - - -
41E ASN* 3.8 31.3 - - - +
42E CYS* 4.4 12.0 - - - -
183E PHE* 4.5 0.6 - - - -
284E ILE* 6.3 2.0 - - + -
285E VAL 3.3 10.5 - - - +
286E ILE* 5.2 1.6 - - + -
299E GLN* 2.9 47.6 + - - +
300E ALA* 1.3 74.3 - - - +
302E THR* 1.3 74.4 + - - +
209G MET* 4.5 14.4 - - - +
211G ILE* 5.8 1.8 - - - +
250G PHE* 3.9 24.2 - - + -
292G GLU* 4.6 13.7 + - - -
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Residues in contact with THR 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 4.4 4.0 - - - -
37E SER 4.0 7.0 - - - -
38E LYS* 3.3 28.9 - - + +
39E LYS* 4.2 4.3 - - - +
183E PHE* 3.3 38.2 - - + -
284E ILE* 3.5 6.2 - - - +
285E VAL* 2.9 44.3 + - - +
301E ARG* 1.3 85.3 - - - +
303E SER* 1.3 61.9 + - - +
304E TYR* 3.9 9.3 - - - -
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Residues in contact with SER 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG* 4.9 3.8 + - - -
36E VAL* 3.2 32.8 - - - -
37E SER 4.1 4.8 + - - -
38E LYS* 4.9 7.5 - - - +
282E GLU* 2.8 37.2 + - - +
283E ILE 3.5 10.9 + - - -
284E ILE* 3.6 8.1 - - - +
302E THR* 1.3 75.0 - - - +
304E TYR* 1.3 68.0 + - - +
305E LEU* 4.5 3.5 - - - +
308E GLU* 3.0 14.7 - - - +
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Residues in contact with TYR 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LYS* 5.7 2.2 - - + -
183E PHE* 3.6 10.3 - + + +
184E SER* 2.6 43.5 + - - -
185E LYS 3.6 11.7 - - - -
186E HIS 3.9 13.0 - - - -
187E ALA* 4.1 17.7 - - + -
198E PHE* 5.6 2.9 - - + -
200E LEU* 3.9 21.2 - - + +
201E ARG 5.4 0.2 + - - -
281E LEU* 5.6 0.5 - - - +
282E GLU* 3.9 3.8 - - - -
283E ILE* 3.1 30.9 + - + +
285E VAL* 3.9 19.1 - - + -
302E THR* 3.9 20.9 - - - -
303E SER* 1.3 78.0 - - - +
305E LEU* 1.3 64.8 + - - +
308E GLU* 3.4 22.9 - - + -
309E ILE* 4.4 17.5 - - + +
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Residues in contact with LEU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ARG* 5.8 7.9 - - - +
33E ALA 5.3 5.8 - - - +
34E ARG* 3.8 36.1 - - + +
281E LEU* 3.8 9.2 - - - +
282E GLU* 3.9 28.9 - - + +
303E SER 4.5 2.0 - - - +
304E TYR* 1.3 74.1 - - - +
306E ALA* 1.3 63.0 + - - +
307E ASP* 3.1 22.9 - - - +
308E GLU* 3.0 34.4 + - + +
309E ILE* 3.2 20.2 - - - +
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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