Contacts of the helix formed by residues 225 - 239 (chain A) in PDB entry 1T9A
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 GLU 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A VAL* 5.0 0.2 - - - +
219A MET 4.1 3.5 - - - +
220A VAL* 3.6 11.7 - - + -
221A LYS* 3.3 32.0 + - - +
222A SER* 3.2 28.5 + - - +
224A GLU* 1.3 77.1 - - + +
226A LEU* 1.3 64.3 + - - +
227A PRO* 3.4 2.5 - - - -
228A LEU* 3.3 15.5 + - + +
229A ARG* 3.0 55.8 + - + +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY* 3.3 39.9 - - - +
97A ILE* 4.1 11.0 - - + -
98A PHE* 4.4 7.4 - - + +
220A VAL* 4.0 17.9 - - + -
222A SER 3.5 3.0 + - - -
223A VAL* 3.2 14.9 + - + +
225A GLU* 1.3 77.6 - - - +
227A PRO* 1.3 71.5 - - + +
229A ARG* 3.4 1.4 + - - +
230A ILE* 3.0 49.0 + - + +
249A LEU* 3.8 29.2 - - + -
253A VAL* 5.2 4.5 - - + -
254A THR* 5.1 7.6 - - + -
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Residues in contact with PRO 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.1 6.7 - - + -
97A ILE* 3.8 20.6 - - + -
101A MET* 4.0 22.2 - - + +
223A VAL 3.6 9.4 - - - +
224A GLU 3.7 7.9 - - - +
225A GLU 3.6 2.9 - - - -
226A LEU* 1.3 95.5 - - + +
228A LEU* 1.3 60.5 + - - +
230A ILE* 3.4 1.7 + - - +
231A ASN* 3.0 28.6 + - - -
262A ILE* 3.7 19.3 - - + -
266A THR* 3.2 15.7 - - - +
267A THR* 4.1 10.8 - - + -
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU 5.2 0.4 + - - +
225A GLU* 3.3 18.3 + - + +
226A LEU 3.3 0.4 - - - -
227A PRO* 1.3 80.0 - - - +
229A ARG* 1.3 79.9 + - - +
231A ASN* 3.2 6.7 + - + +
232A GLU* 2.9 53.5 + - + +
266A THR* 3.2 42.7 + - + -
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 4.1 12.9 - - - -
218A VAL* 3.9 34.4 - - + +
220A VAL* 4.0 27.1 - - + -
225A GLU* 3.0 44.4 + - - +
226A LEU 3.9 2.9 - - - +
228A LEU* 1.3 86.4 - - - +
230A ILE* 1.3 63.3 + - + +
232A GLU* 2.6 39.3 + - - +
233A ALA* 2.9 24.9 + - - +
247A VAL* 4.6 4.8 - - + +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 4.1 23.6 - - + -
101A MET* 3.8 39.0 - - + -
102A MET* 4.2 5.4 - - + -
105A GLN* 4.4 6.1 - - + -
187A PHE* 4.0 17.5 - - + -
226A LEU* 3.0 43.0 + - + +
227A PRO* 3.7 4.0 - - + +
229A ARG* 1.3 75.4 - - + +
231A ASN* 1.3 62.0 + - - +
233A ALA* 3.2 7.1 + - - +
234A PHE* 3.1 47.5 + - + -
247A VAL* 5.3 1.8 - - + -
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Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A MET* 3.3 22.3 - - - +
105A GLN* 2.8 32.4 + - - +
227A PRO 3.0 13.9 + - - +
228A LEU* 3.6 6.5 - - + +
230A ILE* 1.3 77.9 - - - +
232A GLU* 1.3 62.5 + - + +
234A PHE* 3.6 1.7 + - - +
235A GLU* 3.2 24.3 + - - +
266A THR* 3.0 29.0 + - - +
267A THR 3.6 12.7 - - - -
268A LEU 3.8 4.6 + - - +
269A PRO* 3.6 18.8 - - + +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 3.5 18.8 - - + -
228A LEU* 2.9 40.0 + - + +
229A ARG* 2.6 45.4 + - - +
231A ASN* 1.3 75.7 - - + +
233A ALA* 1.3 57.5 + - - +
235A GLU* 3.3 6.7 + - - +
236A ILE* 2.9 40.4 + - + +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 4.0 9.2 - - + -
216A TRP* 3.6 12.3 - - + -
229A ARG 2.9 17.7 + - - +
230A ILE* 3.4 6.5 - - - +
232A GLU* 1.3 76.8 - - - +
234A PHE* 1.3 62.5 + - - +
237A ALA* 3.0 25.6 + - - +
245A VAL* 3.5 21.2 - - + +
247A VAL* 3.7 26.2 - - + -
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Residues in contact with PHE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A MET* 4.1 7.6 - - + -
105A GLN* 3.3 42.6 - - + +
107A VAL* 3.6 33.4 - - + -
156A PRO* 3.9 24.5 - - + -
158A VAL* 3.9 14.6 - - + -
185A VAL* 3.8 26.0 - - + -
187A PHE* 4.1 15.5 - + - -
230A ILE* 3.1 38.4 + - + +
231A ASN 4.2 0.4 - - - +
233A ALA* 1.3 78.8 - - - +
235A GLU* 1.3 61.1 + - - +
237A ALA* 4.0 0.4 - - - +
238A THR* 2.8 33.1 + - + +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASN 3.2 18.6 + - - +
232A GLU* 3.7 5.8 - - - +
233A ALA 3.2 0.2 - - - -
234A PHE* 1.3 79.0 - - - +
236A ILE* 1.3 61.3 + - + +
238A THR* 3.7 4.5 + - - -
239A SER* 2.7 42.5 + - - +
269A PRO 5.6 5.9 - - - -
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 2.8 52.8 + - + +
216A TRP* 3.5 56.8 - - + -
232A GLU* 2.9 22.4 + - + +
233A ALA 4.0 2.7 - - - +
235A GLU* 1.3 83.2 - - + +
237A ALA* 1.3 59.9 + - - +
238A THR 3.5 0.3 + - - -
239A SER* 3.7 6.7 - - - +
245A VAL* 4.0 4.9 - - + -
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PRO* 5.2 0.4 - - + -
183A PRO* 3.4 6.3 - - - +
184A MET 4.0 16.6 - - - +
185A VAL* 4.2 9.6 - - + -
233A ALA 3.0 19.0 + - - +
234A PHE 4.0 3.4 - - - +
236A ILE* 1.3 79.1 - - - +
238A THR* 1.3 62.7 + - + +
242A PRO* 3.3 6.1 - - - +
243A GLY 3.1 43.3 + - - +
245A VAL* 3.9 11.2 - - + +
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Residues in contact with THR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLY 5.9 1.1 - - - +
156A PRO* 3.9 38.6 - - + -
183A PRO* 4.1 9.0 - - + -
234A PHE* 2.8 23.5 + - + +
235A GLU* 3.7 5.2 + - - -
237A ALA* 1.3 81.5 - - + +
239A SER* 1.3 58.9 + - - +
240A GLY 5.0 0.3 - - - +
242A PRO* 4.7 11.1 - - - +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 2.8 22.3 + - - -
235A GLU* 2.7 31.1 + - - +
236A ILE* 3.9 5.7 + - - -
237A ALA 3.6 0.2 - - - -
238A THR* 1.3 78.4 - - - +
240A GLY* 1.3 71.5 + - - +
241A ARG 3.2 4.0 + - - +
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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