Contacts of the helix formed by residues 247 - 259 (chain G) in PDB entry 2VT5
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 SER 247 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121G ASP 4.0 1.7 + - - -
122G GLY* 3.7 21.9 - - - -
130G VAL* 3.9 15.5 - - - -
131G SER 2.5 31.7 + - - -
132G VAL* 3.9 3.6 - - - -
245G VAL* 3.2 5.6 - - - -
246G GLY* 1.3 80.5 - - - +
248G MET* 1.3 65.3 + - - +
249G VAL* 3.4 3.5 + - - +
250G ALA* 3.1 14.8 + - - +
251G ASP* 3.2 15.0 + - - +
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Residues in contact with MET 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ASP* 3.5 18.8 + - - +
135G ILE* 3.9 21.3 - - - -
246G GLY 4.1 0.8 - - - -
247G SER* 1.3 73.1 + - - +
249G VAL* 1.3 58.5 + - - +
251G ASP* 3.9 5.1 - - - +
252G VAL* 2.8 48.9 + - + +
262G PHE* 4.2 14.1 - - + -
275G LEU* 3.7 33.9 - - + -
280G GLU* 3.8 29.2 - - - +
281G CYS* 4.6 5.4 - - - +
284G MET* 3.7 27.6 - - + -
316G VAL* 4.8 2.5 - - + -
318G LEU* 4.5 7.2 - - + -
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Residues in contact with VAL 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ASP* 4.2 8.0 + - + +
132G VAL 4.7 1.1 - - - +
133G GLY* 3.8 25.1 - - - +
134G THR 4.5 0.2 - - - +
135G ILE* 3.5 34.5 - - + -
164G TYR* 3.3 32.2 - - + -
165G ALA 3.6 13.2 - - - +
166G LEU* 3.8 16.4 - - + -
247G SER* 3.4 2.0 + - - +
248G MET* 1.3 75.2 - - - +
250G ALA* 1.3 53.7 + - - +
252G VAL* 4.0 0.3 - - - +
253G HIS* 2.7 37.4 + - - +
284G MET* 3.9 6.5 - - + -
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Residues in contact with ALA 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G SER* 3.7 29.6 - - - +
166G LEU* 3.8 11.9 - - + +
245G VAL* 3.9 21.8 - - + -
247G SER* 3.1 13.4 + - - +
249G VAL* 1.3 74.1 - - - +
251G ASP* 1.3 60.7 + - - +
253G HIS* 3.4 3.2 + - - +
254G ARG* 3.0 31.3 + - - +
128H CYS* 5.0 3.3 - - - +
130H VAL* 6.5 0.9 - - - -
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Residues in contact with ASP 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G SER* 3.5 11.3 + - - +
244G TYR* 3.9 7.8 - - - -
245G VAL* 2.9 18.6 + - - +
246G GLY* 3.2 23.7 + - - -
247G SER 3.2 15.9 + - - +
248G MET 3.9 1.3 - - - +
250G ALA* 1.3 71.9 - - - +
252G VAL* 1.3 60.7 + - - +
254G ARG* 2.3 40.7 + - - +
255G THR* 2.8 33.0 + - - -
262G PHE* 3.7 25.4 - - + -
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Residues in contact with VAL 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G TYR* 4.4 9.0 - - + +
248G MET* 2.8 53.1 + - + +
249G VAL 4.0 1.8 - - - +
251G ASP* 1.3 69.1 - - - +
253G HIS* 1.3 67.7 + - - +
255G THR* 3.1 8.6 + - - -
256G LEU* 3.0 21.0 + - - +
262G PHE* 4.6 7.2 - - + -
284G MET* 3.6 34.1 - - + -
287G VAL* 5.8 1.1 - - + -
288G MET* 3.9 19.4 - - + +
318G LEU* 4.4 16.4 - - + -
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Residues in contact with HIS 253 (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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164G TYR* 2.7 36.5 + + + +
166G LEU* 3.6 20.0 - - + -
172G MET* 3.6 32.6 - - + +
174G VAL* 3.9 7.4 - - + -
183G CYS* 5.0 5.4 - - - -
249G VAL 2.7 23.6 + - - +
250G ALA 3.9 3.6 - - - +
252G VAL* 1.3 74.0 - - - +
254G ARG* 1.3 60.1 + - - +
256G LEU* 3.2 7.8 + - + +
257G VAL* 3.0 42.9 + - + +
127H ASP 4.6 2.4 + - - -
128H CYS* 3.2 31.6 - - - -
129H LEU* 4.4 4.2 - - + +
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Residues in contact with ARG 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G ILE* 3.9 32.9 - - - +
210G SER* 3.6 22.8 + - - -
243G ARG* 3.4 33.8 + - - +
245G VAL* 3.9 12.3 - - - +
250G ALA 3.0 14.4 + - - +
251G ASP* 2.3 50.4 + - - +
252G VAL 3.3 0.2 - - - -
253G HIS* 1.3 75.8 - - - +
255G THR* 1.3 61.4 + - - +
257G VAL 3.2 0.2 + - - -
258G TYR* 2.7 44.8 + - + +
259G GLY 5.1 0.7 - - - -
125H ASN* 5.9 2.9 - - - +
128H CYS* 3.7 37.3 - - - +
245H VAL 5.5 1.4 + - - -
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Residues in contact with THR 255 (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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202G ILE* 3.3 6.0 - - + +
251G ASP 2.8 20.9 + - - -
252G VAL* 3.1 11.4 + - - -
254G ARG* 1.3 85.9 + - - +
256G LEU* 1.3 57.8 + - - +
259G GLY* 2.9 33.5 + - - -
260G GLY 3.4 30.3 - - - +
261G ILE* 4.1 5.9 + - - +
262G PHE* 4.0 11.8 - - - +
288G MET* 4.4 4.5 - - + -
318G LEU* 4.3 6.3 - - + +
319G GLY* 3.7 20.0 - - - -
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Residues in contact with LEU 256 (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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164G TYR* 3.5 20.0 - - + +
174G VAL* 4.0 20.2 - - + -
181G VAL* 4.4 1.3 - - + -
183G CYS* 5.0 3.8 - - - -
200G VAL* 3.8 26.5 - - + +
201G LYS 4.9 2.1 - - - +
202G ILE* 4.0 28.1 - - + +
203G LYS 5.0 0.7 + - - -
252G VAL 3.0 12.0 + - - +
253G HIS* 3.5 13.0 - - + +
255G THR* 1.3 77.2 - - - +
257G VAL* 1.3 65.0 + - + +
259G GLY 4.3 0.5 + - - -
287G VAL* 4.1 12.8 - - + -
288G MET* 4.0 13.6 - - + +
291G ALA* 3.6 30.3 - - + -
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Residues in contact with VAL 257 (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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183G CYS* 6.3 1.1 - - - -
200G VAL* 6.5 0.4 - - + -
203G LYS* 4.7 8.3 - - - +
253G HIS* 3.0 46.2 + - + +
254G ARG 3.9 2.5 - - - +
256G LEU* 1.3 83.7 - - + +
258G TYR* 1.3 77.5 + - + +
259G GLY 3.9 0.2 + - - -
127H ASP* 3.7 28.9 - - + +
128H CYS* 4.2 4.5 - - + -
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Residues in contact with TYR 258 (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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203G LYS* 3.0 37.0 + - - +
206G GLY* 4.5 4.0 - - - -
207G LYS 5.1 1.4 + - - -
208G ILE* 4.6 14.8 - - + -
254G ARG* 2.7 29.4 + - + +
257G VAL* 1.3 80.6 - - + +
259G GLY* 1.3 62.9 + - - +
124H SER 3.5 3.7 + - - -
125H ASN* 3.2 31.2 - - + -
127H ASP* 2.7 31.8 + - + -
128H CYS* 3.5 41.7 - - + -
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Residues in contact with GLY 259 (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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202G ILE* 4.3 5.8 - - - -
203G LYS* 4.3 7.3 - - - +
206G GLY* 3.8 7.5 - - - -
207G LYS 4.6 0.3 + - - -
208G ILE* 4.2 13.5 + - - +
254G ARG* 5.1 0.5 - - - -
255G THR* 2.9 28.1 + - - +
256G LEU 4.3 1.2 + - - -
257G VAL 3.5 2.0 - - - -
258G TYR* 1.3 88.1 - - - +
260G GLY* 1.3 59.5 + - - -
320G SER* 3.5 11.4 - - - -
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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