Contacts of the helix formed by residues 295 - 312 (chain A) in PDB entry 1TYI
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 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A SER* 5.3 0.9 - - - +
259A GLY* 4.4 11.1 + - - -
260A ASP* 3.6 19.0 + - + +
261A ARG* 5.0 14.5 + - - +
294A TYR* 1.3 76.8 - - - +
296A ILE* 1.3 61.2 + - - +
297A ARG* 3.8 13.7 + - - -
298A ASN* 2.7 44.7 + - + +
299A VAL* 2.8 35.0 + - + +
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 4.5 23.8 - - + -
24A HIS* 4.4 10.1 - - + +
28A MET* 3.6 40.8 - - + -
261A ARG* 5.9 4.9 - - - +
294A TYR 3.7 6.0 + - - +
295A THR* 1.3 77.5 + - - +
297A ARG* 1.4 83.9 + - - +
299A VAL* 3.8 4.9 - - - +
300A ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A MET* 5.6 3.6 - - - +
295A THR* 3.3 10.7 - - - +
296A ILE* 1.4 107.7 - - - +
298A ASN* 1.3 64.7 + - - +
300A ALA* 3.8 3.6 - - - +
301A ARG* 2.9 45.1 + - + +
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Residues in contact with ASN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER* 3.7 3.8 - - - +
257A LEU* 3.5 35.3 - - + +
258A SER 5.0 0.4 - - - +
259A GLY* 3.7 21.5 - - - +
269A ILE* 5.2 1.8 - - - +
295A THR* 2.7 38.1 + - + +
297A ARG* 1.3 79.3 - - - +
299A VAL* 1.3 66.9 + - - +
301A ARG* 3.3 29.2 + - - +
302A CYS* 2.8 29.5 + - - +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 4.6 14.6 - - + +
29A THR* 4.3 4.9 - - - +
254A SER* 3.6 11.9 - - - +
293A GLY* 3.6 37.7 - - - +
295A THR* 2.8 30.8 + - + +
296A ILE* 3.8 5.8 - - - +
298A ASN* 1.3 76.4 - - - +
300A ALA* 1.3 63.7 + - - +
303A TRP* 3.0 64.6 + - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A MET* 3.8 21.3 - - + -
29A THR* 4.4 8.2 - - - +
32A LEU* 3.1 30.8 - - + +
36A TYR* 5.3 0.2 - - - +
296A ILE 2.9 18.3 + - - +
297A ARG* 3.9 3.6 - - - +
299A VAL* 1.3 79.2 - - - +
301A ARG* 1.4 58.3 + - - +
303A TRP* 4.3 0.7 - - - +
304A THR* 2.6 32.7 + - - -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 5.0 0.9 - - - -
36A TYR* 5.3 3.6 - - - +
269A ILE* 3.3 29.5 - - + +
297A ARG* 2.9 30.3 + - + +
298A ASN* 3.3 30.0 + - - +
300A ALA* 1.4 75.7 - - + +
302A CYS* 1.3 58.9 + - - +
304A THR* 3.1 8.2 + - - -
305A TYR* 2.8 38.4 + - + -
319A LEU* 4.4 25.4 - - + -
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Residues in contact with CYS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER* 3.8 9.0 - - - +
257A LEU* 3.7 20.9 - - + -
269A ILE* 4.1 6.7 - - + -
272A HIS* 3.1 47.5 - - - -
298A ASN 2.8 20.7 + - - +
299A VAL 3.8 0.7 - - - +
301A ARG* 1.3 77.7 - - - +
303A TRP* 1.3 71.7 + - + +
305A TYR* 3.0 23.3 + - - +
306A GLU* 3.3 10.6 + - - +
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Residues in contact with TRP 303 (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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4A TYR* 3.8 15.8 + - - +
25A ARG* 2.9 46.0 - - - -
29A THR* 3.5 23.6 - - + -
126A TRP* 3.4 43.7 - + + -
252A CYS* 3.6 19.2 + - + -
254A SER* 3.7 17.7 - - - +
272A HIS* 5.3 0.2 - - - -
290A GLY* 4.7 1.3 - - - -
291A GLY 3.9 15.0 - - - -
292A GLY 4.8 0.9 - - - -
299A VAL* 3.0 39.0 + - + +
300A ALA 4.3 1.3 - - - +
302A CYS* 1.3 86.4 - - + +
304A THR* 1.3 60.3 + - - +
306A GLU* 3.1 15.8 + - + +
307A THR* 2.9 25.5 + - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 4.6 1.3 - - - +
32A LEU* 2.9 20.8 - - - +
33A LEU* 3.2 11.8 - - + +
36A TYR* 4.4 5.6 - - + -
38A LEU* 3.0 36.3 - - + -
300A ALA 2.6 22.8 + - - -
301A ARG* 3.1 7.6 + - - -
303A TRP* 1.3 76.0 - - - +
305A TYR* 1.3 62.8 + - - +
307A THR* 2.7 26.1 - - - +
308A ALA* 2.9 7.8 + - - +
315A ILE* 4.3 9.9 - - + -
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Residues in contact with TYR 305 (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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269A ILE* 2.9 49.7 - - + +
270A LYS* 5.9 3.6 - - + -
272A HIS* 6.4 0.2 - - + -
273A ALA* 4.5 20.2 - - + -
301A ARG* 2.8 34.8 + - + -
302A CYS 3.0 8.2 + - - +
304A THR* 1.3 76.5 - - - +
306A GLU* 1.3 59.2 + - + +
308A ALA* 3.3 1.9 + - - +
309A VAL* 2.9 37.2 + - + +
315A ILE* 3.5 41.3 - - + +
316A PRO 5.4 1.9 + - - -
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 5.8 0.9 - - + +
124A VAL* 5.5 14.7 - - + +
252A CYS* 4.9 9.6 - - + -
272A HIS* 3.2 23.3 - - + +
273A ALA* 4.2 6.1 - - - -
276A VAL* 2.7 48.3 - - - +
280A LYS* 4.8 0.2 + - - -
288A MET* 5.7 3.8 - - - +
302A CYS 3.7 12.3 - - - +
303A TRP* 3.1 18.1 + - + +
305A TYR* 1.3 79.3 - - - +
307A THR* 1.3 60.4 + - - +
309A VAL* 2.7 29.5 - - - +
310A ALA* 3.1 9.4 + - - +
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Residues in contact with THR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 5.3 1.6 - - - +
4A TYR* 4.2 22.3 + - - -
33A LEU* 3.6 36.2 - - + +
38A LEU* 4.9 4.7 - - + -
39A TYR* 4.9 4.7 - - - -
124A VAL* 6.0 1.8 - - - -
303A TRP 2.9 9.9 + - - +
304A THR* 2.7 37.2 - - + +
306A GLU* 1.3 78.8 - - - +
308A ALA* 1.3 52.3 + - + +
310A ALA* 3.3 4.4 + - - +
311A LEU* 2.6 48.3 + - + +
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Residues in contact with ALA 308 (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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38A LEU* 5.5 4.3 - - + -
304A THR* 2.9 17.6 + - + +
305A TYR* 3.7 4.0 - - - +
307A THR* 1.3 75.4 - - + +
309A VAL* 1.3 57.3 + - + +
311A LEU* 3.9 8.3 - - - -
312A ASP* 2.6 30.7 + - - -
313A THR* 3.0 31.9 + - - +
314A GLU 4.9 0.9 - - - +
315A ILE* 3.9 25.4 - - + -
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 5.1 10.3 - - + -
277A GLU* 3.7 29.2 - - + +
280A LYS* 3.8 16.4 - - - +
305A TYR* 2.9 24.0 + - + +
306A GLU* 2.7 38.6 - - - +
308A ALA* 1.3 78.3 - - + +
310A ALA* 1.3 62.3 + - + +
312A ASP* 2.8 23.1 + - - +
313A THR 5.3 0.2 - - - -
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Residues in contact with ALA 310 (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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2A VAL* 2.9 41.0 - - + +
122A ILE* 4.7 10.7 - - + +
124A VAL* 4.8 11.4 - - + -
280A LYS* 5.5 7.2 - - - +
288A MET* 5.2 8.1 - - + -
306A GLU 3.1 11.8 + - - +
307A THR* 3.8 3.8 - - - +
309A VAL* 1.3 79.0 - - + +
311A LEU* 1.3 61.4 + - - +
312A ASP* 2.9 16.4 + - - +
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Residues in contact with LEU 311 (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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2A VAL* 4.3 13.1 - - + +
38A LEU* 2.7 36.3 - - + +
43A GLU* 3.4 26.2 - - - +
307A THR* 2.6 32.2 + - + +
308A ALA* 3.6 6.5 - - - +
310A ALA* 1.3 69.5 - - - +
312A ASP* 1.3 67.7 + - - +
313A THR* 3.0 35.9 - - + +
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Residues in contact with ASP 312 (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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2A VAL* 5.0 3.8 - - - +
308A ALA 2.6 10.0 + - - -
309A VAL* 2.8 18.9 - - - +
310A ALA* 2.9 14.3 - - - +
311A LEU* 1.3 79.8 - - - +
313A THR* 1.3 59.5 + - - +
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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
------------------------------------------------------------
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