Contacts of the strand formed by residues 297 - 304 (chain G) in PDB entry 5YWB
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 3.9 12.7 - - - +
290A VAL* 3.5 41.0 - - + +
291A VAL 5.3 2.1 - - - +
292A GLU* 5.3 6.9 - - - +
295A GLY 5.1 3.8 - - - +
288G GLU* 3.6 19.6 + - - +
289G GLY 3.6 5.2 - - - -
290G VAL* 3.9 11.2 - - + +
295G GLY 4.5 4.0 - - - +
296G ILE* 1.3 83.2 - - - +
298G THR* 1.3 62.8 + - - +
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Residues in contact with THR 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G ALA* 3.7 33.3 - - + +
181G LEU* 6.1 2.0 - - + -
210G ILE* 5.0 4.3 - - - +
288G GLU* 3.6 2.6 - - - +
289G GLY 2.9 33.8 + - - +
291G VAL* 4.1 14.5 - - - +
296G ILE* 3.5 20.0 + - + +
297G THR* 1.3 75.9 - - - +
299G GLN* 1.3 75.2 + - - +
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Residues in contact with GLN 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A MET* 4.0 10.8 - - - +
211A ILE* 4.3 26.8 - - + +
212A SER 4.6 3.8 - - - +
250A PHE* 3.8 9.1 - - - -
292A GLU* 5.5 3.3 - - + +
178G ALA 5.4 0.9 - - - +
181G LEU* 5.3 6.0 - - - +
210G ILE* 6.2 0.7 - - - -
216G HIS* 5.8 1.0 - - - -
286G ILE* 3.4 25.5 - - + +
287G LEU 3.0 14.6 - - - +
288G GLU* 3.8 15.2 - - + +
298G THR* 1.3 87.6 - - - +
300G ALA* 1.3 63.4 + - - +
301G ARG* 3.2 42.3 + - - +
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Residues in contact with ALA 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G LEU* 3.5 38.1 - - + -
183G PHE* 3.8 18.9 - - + -
285G VAL 3.5 2.3 - - - +
286G ILE* 3.5 1.0 - - - -
287G LEU* 2.8 36.9 + - + +
299G GLN* 1.3 76.2 - - - +
301G ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A MET* 3.8 25.7 - - - +
250A PHE* 4.1 13.2 - - + -
252A VAL* 6.2 0.2 - - - -
292A GLU* 4.0 11.6 + - - -
36G VAL* 5.2 13.0 - - + -
37G SER 4.2 1.1 - - - +
38G LYS 4.2 0.9 - - - +
39G LYS 4.7 0.2 - - - -
40G GLY* 3.2 57.1 + - - +
41G ASN* 5.2 4.4 - - - +
42G CYS* 5.6 2.8 - - - +
183G PHE* 5.5 0.2 - - - -
285G VAL 3.2 4.3 - - - -
286G ILE* 3.6 29.6 - - + -
299G GLN* 3.2 41.9 + - - +
300G ALA* 1.3 75.0 - - - +
302G THR* 1.3 63.2 + - - +
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Residues in contact with THR 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G VAL* 5.1 0.9 - - - -
37G SER 4.6 4.7 - - - -
38G LYS* 3.8 23.5 + - - +
183G PHE* 3.9 25.9 - - + +
283G ILE 3.9 0.5 - - - +
284G ILE* 3.0 6.4 - - - +
285G VAL* 2.9 54.4 + - + -
286G ILE* 5.1 0.2 - - - +
300G ALA 4.2 0.2 - - - -
301G ARG* 1.3 75.9 - - - +
303G SER* 1.3 69.5 + - - +
304G TYR* 3.5 21.8 + - + +
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Residues in contact with SER 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ARG* 6.0 2.0 - - - -
35G PHE* 4.9 1.7 - - - +
36G VAL* 2.5 50.8 + - - +
37G SER 4.6 2.7 + - - -
38G LYS* 3.3 30.9 + - - +
282G GLU* 5.1 7.9 - - - -
283G ILE 3.6 4.5 - - - -
284G ILE* 3.2 9.8 - - - +
302G THR* 1.3 74.6 + - - +
304G TYR* 1.3 68.7 + - - +
305G LEU* 4.3 8.5 - - - -
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Residues in contact with TYR 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LYS* 3.7 9.6 - - - +
183G PHE* 3.1 21.3 - - - +
184G SER 2.6 21.6 + - - -
185G LYS 3.1 30.3 - - - -
186G HIS* 4.0 4.9 - - - -
187G ALA* 4.0 19.3 - - + -
198G PHE* 5.5 3.6 - + + -
200G LEU* 3.2 31.6 - - + +
281G LEU 3.4 2.8 - - - +
282G GLU* 3.4 0.6 - - - -
283G ILE* 2.9 50.9 + - + +
285G VAL* 4.9 3.6 - - + -
302G THR* 3.5 24.1 + - + -
303G SER* 1.3 76.2 - - - +
305G LEU* 1.3 68.8 + - - +
308G GLU* 4.7 6.3 - - + -
309G ILE* 5.3 8.7 - - + -
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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