Contacts of the helix formed by residues 293 - 308 (chain B) in PDB entry 1TW2
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 ASN 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA* 3.6 11.9 - - - +
284B ARG* 5.3 1.0 + - - -
290B ASN* 2.9 30.9 + - - +
291B SER 3.3 1.9 + - - -
292B PHE* 1.3 79.0 - - - +
294B GLU* 1.3 64.6 + - - +
295B GLN* 3.2 21.5 + - - +
296B PHE* 3.2 31.7 + - - +
297B THR* 3.2 15.7 + - - +
340B PRO* 5.9 1.5 - - - +
341B TYR* 5.8 1.0 - - - +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.8 39.2 + - - +
27A THR* 5.5 1.2 + - - -
70A HIS* 4.7 13.7 - - - +
73A ALA* 4.2 20.8 - - + +
74A ILE* 4.7 10.8 - - + +
293B ASN* 1.3 74.0 - - - +
295B GLN* 1.3 79.3 + - - +
296B PHE 3.1 1.1 - - - -
297B THR* 3.4 10.5 - - - +
298B GLU* 3.1 47.5 + - - +
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Residues in contact with GLN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 4.3 30.2 + - - +
21A ARG* 5.1 4.0 - - - +
284B ARG* 3.1 23.5 + - - -
293B ASN* 3.2 23.7 - - - +
294B GLU* 1.3 103.3 + - + +
296B PHE* 1.3 56.3 + - - +
298B GLU* 4.7 7.2 + - - +
299B LEU* 5.2 3.5 + - - +
339B ILE* 6.4 0.7 - - + -
340B PRO* 4.3 21.4 - - + +
341B TYR* 3.9 21.1 - - + -
1600B ERT 6.4 1.1 - - - -
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Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.5 37.5 - - - -
284B ARG* 3.7 18.8 - - - +
286B ASP* 3.9 22.9 - - + +
290B ASN 5.2 0.2 - - - +
291B SER* 3.6 33.9 - - - +
293B ASN* 3.2 17.1 + - - +
294B GLU 3.1 0.4 - - - -
295B GLN* 1.3 78.3 - - - +
297B THR* 1.3 64.0 + - - +
298B GLU 3.3 2.0 + - - -
299B LEU* 3.6 2.4 + - - +
300B ASP* 3.1 40.1 + - + +
311B LEU* 3.4 40.9 - - + +
312B ARG 5.5 0.9 - - - -
313B THR* 4.5 12.3 - - + -
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Residues in contact with THR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 4.5 1.3 - - - -
66A ARG 4.7 1.8 - - - +
69A ARG* 3.6 35.2 - - + +
70A HIS* 2.9 43.6 - - + +
291B SER 4.1 6.7 - - - +
293B ASN 3.2 16.6 + - - +
294B GLU* 3.4 4.5 - - - -
296B PHE* 1.3 78.6 - - + +
298B GLU* 1.3 61.1 + - - +
300B ASP* 3.7 5.8 - - - +
301B LEU* 2.9 37.6 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.3 33.3 - - - +
24A SER* 4.8 9.5 + - - +
26A HIS* 2.8 46.9 + - + +
70A HIS* 5.3 2.9 - - - +
294B GLU* 3.1 36.9 + - + +
295B GLN* 4.7 6.3 - - - +
296B PHE 3.3 0.2 - - - -
297B THR* 1.3 75.8 + - - +
299B LEU* 1.3 63.9 + - - +
302B ARG* 3.0 24.3 + - - +
1600B ERT 4.0 24.9 - - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 4.2 10.1 - - + -
255B LEU* 3.8 27.4 - - + -
284B ARG* 4.3 16.4 - - - +
295B GLN 5.2 2.6 + - - +
296B PHE 3.6 3.6 + - - +
298B GLU* 1.3 78.6 - - - +
300B ASP* 1.3 64.0 + - - +
302B ARG* 3.7 4.4 - - + +
303B MET* 3.0 27.5 + - - +
311B LEU* 3.9 20.0 - - + -
1600B ERT 3.5 71.6 + - + +
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Residues in contact with ASP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 2.9 71.4 + - - +
69A ARG* 4.6 1.3 + - - -
296B PHE* 3.1 43.6 + - + +
297B THR* 4.1 4.8 - - - +
298B GLU 3.3 0.2 - - - -
299B LEU* 1.3 78.9 - - - +
301B LEU* 1.3 60.4 + - - +
303B MET* 3.3 5.1 + - - +
304B LEU 3.1 12.5 + - - -
310B ALA* 3.6 1.9 - - - +
311B LEU* 3.0 33.1 + - + +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 4.1 7.4 - - + -
30A VAL* 4.2 17.3 - - + -
66A ARG* 3.9 36.8 - - + +
67A LEU* 4.5 4.7 - - + +
70A HIS* 4.0 27.4 - - + -
119B PHE* 3.7 17.7 - - + -
122B LEU* 5.0 7.0 - - + -
126B ILE* 5.2 2.0 - - + -
297B THR* 2.9 22.9 + - - +
300B ASP* 1.3 74.7 - - - +
302B ARG* 1.3 66.1 + - - +
303B MET 3.1 0.9 - - - -
304B LEU* 3.2 22.9 + - + +
305B VAL* 3.0 27.4 + - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 3.4 24.5 + - + -
32B ARG* 4.4 6.7 - - - +
105B TRP* 4.6 8.5 + - - +
112B VAL* 4.1 12.4 - - - +
116B ASP* 2.8 32.2 + - - -
119B PHE* 3.5 7.7 - - + -
298B GLU* 3.0 31.4 + - - +
299B LEU* 3.7 9.0 - - + +
301B LEU* 1.3 74.3 - - - +
303B MET* 1.3 59.3 + - - +
306B PHE* 2.8 75.0 + - + +
1600B ERT 3.4 58.1 + - + +
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Residues in contact with MET 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 2.9 44.9 - - + +
256B ASN* 3.4 23.6 - - - +
299B LEU* 3.0 25.2 + - - +
300B ASP* 3.5 7.4 - - - +
301B LEU 3.1 0.4 - - - -
302B ARG* 1.3 79.1 - - - +
304B LEU* 1.3 62.5 + - - +
306B PHE* 4.8 0.2 - - + -
307B LEU* 2.8 47.7 + - + +
308B GLY 3.0 6.8 + - - -
309B GLY 3.0 27.1 + - - -
310B ALA* 3.9 4.3 - - - +
311B LEU 5.0 0.4 - - - +
1600B ERT 3.5 20.6 - - + -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA* 4.8 7.2 - - + +
66A ARG* 3.5 32.1 - - + +
122B LEU* 4.3 6.1 - - + -
125B ALA* 4.0 26.7 - - + +
126B ILE* 4.1 18.4 - - + -
129B GLY* 3.8 30.1 - - - +
131B PRO* 3.4 11.3 - - - +
300B ASP 3.1 7.7 + - - +
301B LEU* 3.2 28.7 + - + +
303B MET* 1.3 75.3 - - - +
305B VAL* 1.3 59.6 + - - +
308B GLY* 3.1 21.6 + - - +
309B GLY 3.4 8.4 + - - +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER* 3.3 42.8 - - - +
119B PHE* 3.9 13.0 - - + +
122B LEU* 3.6 31.6 - - + -
125B ALA* 3.9 14.6 - - + -
131B PRO* 4.3 0.4 - - - -
132B THR* 2.9 31.7 + - - +
133B TYR* 3.3 7.1 + - - +
301B LEU 3.0 12.7 + - - +
304B LEU* 1.3 78.4 - - + +
306B PHE* 1.3 78.2 + - + +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 3.8 8.7 - - + -
115B ALA* 3.2 51.1 - - + -
116B ASP* 3.3 24.9 - - - -
118B SER* 4.3 1.1 - - - -
119B PHE* 4.4 1.1 - + - -
131B PRO* 3.8 5.5 - - - +
133B TYR* 3.5 21.6 - + - +
141B PHE* 3.8 21.7 + + + +
302B ARG* 2.8 45.6 + - + +
303B MET* 5.1 0.2 - - + -
305B VAL* 1.3 93.4 - - + +
307B LEU* 1.3 73.2 + - + +
1600B ERT 3.9 31.4 - + - -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PRO* 3.7 12.2 - - - +
141B PHE* 3.9 25.8 - - + +
142B TYR* 3.7 25.8 - - + -
256B ASN* 3.5 30.7 - - + +
257B TRP* 5.1 9.6 - - + -
258B PRO* 4.4 7.3 - - - +
303B MET* 2.8 39.1 + - + +
305B VAL 3.5 0.4 - - - -
306B PHE* 1.3 87.7 - - + +
308B GLY* 1.3 61.1 + - - +
309B GLY 3.5 1.0 + - - +
1600B ERT 4.0 13.7 - - + -
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Residues in contact with GLY 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 5.0 3.0 + - - -
129B GLY 4.5 11.0 - - - +
131B PRO* 3.6 17.7 - - - +
258B PRO* 3.5 28.1 - - - +
303B MET 3.0 3.4 + - - -
304B LEU* 3.1 16.8 + - - -
307B LEU* 1.3 77.4 - - - +
309B GLY* 1.3 62.9 + - - +
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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
------------------------------------------------------------
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