Contacts of the helix formed by residues 277 - 292 (chain H) in PDB entry 1I43
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 PRO 277 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H GLU* 3.6 17.5 - - + +
248H LEU* 5.2 1.1 - - + -
253H ASP* 3.0 23.1 - - + +
254H LEU* 4.3 0.2 - - + -
276H GLY* 1.3 86.9 - - - +
278H LEU* 1.3 66.1 + - - +
279H LYS* 4.6 7.0 - - + +
280H LEU* 3.2 29.2 + - + +
281H VAL* 2.9 21.5 + - - +
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Residues in contact with LEU 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H GLU* 2.7 42.3 + - + +
131H SER* 4.4 10.3 - - - -
277H PRO* 1.3 69.4 - - - +
279H LYS* 1.3 65.1 + - - +
280H LEU 2.9 0.5 + - - -
281H VAL* 3.7 8.3 - - + -
282H SER* 2.8 39.9 + - - -
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Residues in contact with LYS 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H GLU* 4.4 1.4 + - - -
277H PRO* 3.4 5.8 - - + -
278H LEU* 1.3 79.7 - - - +
280H LEU* 1.3 67.6 + - + +
282H SER* 3.7 8.1 + - - -
283H GLU* 3.6 17.8 - - - +
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Residues in contact with LEU 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H LEU* 4.1 14.7 - - + +
232H LEU* 3.8 30.7 - - + -
253H ASP* 4.0 14.8 - - + +
254H LEU* 3.8 35.4 - - + -
277H PRO* 3.2 22.9 + - + +
278H LEU 2.9 1.2 + - - -
279H LYS* 1.3 87.5 - - + +
281H VAL* 1.3 60.3 + - - +
282H SER 3.1 1.8 - - - -
283H GLU* 2.8 31.6 + - + +
284H ILE* 3.4 10.1 + - - +
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Residues in contact with VAL 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H SER* 3.1 43.3 - - - +
133H LEU* 3.9 18.7 - - + +
254H LEU* 4.4 3.7 - - + +
274H ILE* 3.8 31.6 - - + +
276H GLY 4.4 4.7 - - - +
277H PRO 2.9 22.1 + - - +
278H LEU* 3.5 6.1 - - + +
280H LEU* 1.3 74.8 - - - +
282H SER* 1.3 68.1 + - - +
284H ILE* 3.4 12.8 + - + +
285H ARG* 3.1 23.4 + - - +
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Residues in contact with SER 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H LEU* 2.8 38.4 + - - -
279H LYS* 3.7 8.5 + - - -
281H VAL* 1.3 73.5 - - - +
283H GLU* 1.3 72.0 + - - +
285H ARG* 3.2 13.3 + - - +
286H ASN* 3.1 29.3 + - - +
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Residues in contact with GLU 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H ALA* 4.4 16.2 - - - +
149H LEU* 4.4 15.0 - - + -
279H LYS 3.6 15.0 - - - +
280H LEU* 2.8 15.7 + - + +
282H SER* 1.3 84.7 + - - +
284H ILE* 1.3 59.5 + - - +
286H ASN* 3.2 29.0 + - - +
287H LEU* 3.5 5.0 + - - +
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Residues in contact with ILE 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H LEU* 3.8 16.6 - - + -
135H MET* 4.1 5.8 - - + -
144H VAL* 3.5 24.9 - - + +
145H MET* 4.1 23.1 - - + -
148H ALA* 4.0 18.4 - - + -
149H LEU* 4.0 26.5 - - + -
254H LEU* 4.5 6.1 - - + -
274H ILE* 4.1 21.3 - - + -
280H LEU 3.4 11.6 + - - +
281H VAL* 3.4 11.8 + - - +
282H SER 3.2 0.4 - - - -
283H GLU* 1.3 72.6 - - - +
285H ARG* 1.3 61.7 + - - +
286H ASN 3.2 0.2 + - - -
287H LEU 3.3 1.9 + - - -
288H HIS* 2.9 25.6 + - - +
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Residues in contact with ARG 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H TYR 5.4 4.3 + - - -
117H VAL* 6.1 0.8 - - - +
120H GLU* 3.1 30.9 + - - -
131H SER* 3.4 23.8 + - - -
132H THR 3.8 14.8 + - - -
133H LEU* 3.8 26.8 - - + +
281H VAL* 3.1 15.6 + - - +
282H SER* 3.2 15.3 + - - +
284H ILE* 1.3 77.5 - - - +
286H ASN* 1.3 61.8 + - - +
288H HIS* 3.2 9.6 - - - +
289H HIS* 3.0 54.7 + - + +
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Residues in contact with ASN 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H SER* 3.1 17.0 + - - +
283H GLU* 3.3 22.2 + - - +
284H ILE 3.1 0.8 - - - -
285H ARG* 1.3 79.5 - - - +
287H LEU* 1.3 65.3 + - - +
288H HIS 3.1 1.3 - - - -
289H HIS* 3.3 24.7 + - - +
290H ILE* 3.7 13.6 + - - +
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Residues in contact with LEU 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ILE* 3.9 31.4 - - + -
144H VAL* 3.6 28.7 - - + +
147H LEU* 3.6 25.8 - - + +
148H ALA* 3.6 19.5 - - + -
283H GLU 3.5 2.9 + - - +
284H ILE 3.3 7.7 + - - +
286H ASN* 1.3 78.3 - - - +
288H HIS* 1.3 57.7 + - - +
290H ILE* 3.1 14.9 + - + +
291H LEU* 3.0 47.5 + - + +
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Residues in contact with HIS 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H ARG* 4.8 5.2 + - - +
133H LEU* 4.1 20.6 - - + -
134H LEU 4.0 9.8 + - - -
135H MET* 3.4 34.6 - - + +
144H VAL* 4.3 12.7 - - + +
284H ILE 2.9 14.7 + - - +
285H ARG* 3.2 11.7 - - - +
286H ASN 3.1 0.2 - - - -
287H LEU* 1.3 74.5 - - - +
289H HIS* 1.3 71.8 + + - +
290H ILE 2.9 5.2 - - - -
291H LEU* 4.5 3.3 - - - +
292H GLY* 2.8 30.7 + - - -
293H GLY* 3.5 34.5 + - - -
294H ALA* 4.0 12.1 + - - +
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Residues in contact with HIS 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F LYS* 4.4 7.3 - - - +
110H ARG* 3.0 51.6 + - - +
111H TYR* 3.5 48.0 + + + -
285H ARG* 3.0 46.5 + - + -
286H ASN* 3.3 17.2 + - - +
288H HIS* 1.3 85.6 - + - +
290H ILE* 1.3 60.8 + - + +
292H GLY 4.3 0.7 - - - -
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Residues in contact with ILE 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET* 3.3 31.4 - - + +
143F THR* 3.8 0.5 + - - -
165F LYS* 4.4 25.4 - - + +
168F ILE* 4.0 26.9 - - + -
169F PHE* 4.0 37.0 - - + +
172F THR* 5.5 1.8 - - - +
173F ILE* 5.6 3.4 - - + -
286H ASN 3.9 13.5 - - - +
287H LEU* 3.1 19.2 + - + +
288H HIS 2.9 0.4 - - - -
289H HIS* 1.3 81.5 - - + +
291H LEU* 1.3 65.3 + - + +
292H GLY 3.0 5.4 + - - -
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Residues in contact with LEU 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET 4.5 0.2 - - - -
140F CYS* 3.1 29.1 - - - +
143F THR* 3.4 31.9 + - + +
147F LEU* 4.9 3.6 - - + -
169F PHE* 3.7 21.8 - - + -
173F ILE* 5.9 0.7 - - + -
291F LEU* 6.5 1.6 - - + -
143H THR* 5.2 2.0 - - + -
144H VAL* 3.6 31.4 - - + -
147H LEU* 4.2 17.7 - - + -
287H LEU* 3.0 41.4 + - + +
288H HIS* 4.3 2.0 - - - +
290H ILE* 1.3 75.9 - - + +
292H GLY* 1.3 63.8 + - - +
293H GLY 5.0 1.6 - - - +
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Residues in contact with GLY 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ALA* 3.7 3.5 - - - +
137F SER* 2.9 27.6 + - - -
139F MET* 4.4 0.9 - - - -
140F CYS* 3.1 16.8 - - - +
110H ARG* 3.8 19.3 - - - -
288H HIS* 2.8 15.4 + - - -
290H ILE 3.0 3.6 - - - -
291H LEU* 1.3 76.2 - - - +
293H GLY* 1.3 56.6 + - - +
294H ALA 3.3 7.1 + - - -
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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
------------------------------------------------------------
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