Contacts of the helix formed by residues 239 - 254 (chain A) in PDB entry 3SMT
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 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLN* 3.8 30.7 - - + +
64A LYS* 4.2 10.1 - - + +
65A GLY 2.5 30.2 + - - +
67A SER* 4.0 11.4 - - - +
216A TYR* 3.2 15.4 - - - -
237A SER* 4.0 9.2 - - - +
238A PHE* 1.3 74.4 - - - +
240A TYR* 1.4 63.5 + - - +
241A GLU* 3.7 2.7 + - - -
242A ASP* 3.1 36.9 + - - +
243A TYR 3.3 3.3 + - - -
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Residues in contact with TYR 240 (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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31A LEU* 5.7 0.9 - - + -
56A VAL* 3.5 38.1 - - + +
57A GLU* 5.5 0.4 - - - -
59A ILE* 5.7 2.5 - - + -
60A ARG* 4.1 22.0 - - + +
63A GLN* 3.0 19.8 + - - +
186A LEU* 4.4 11.1 + - - +
209A TYR* 4.0 22.2 + - - -
212A THR* 4.6 15.6 - - + +
213A ALA* 4.8 9.1 - - - +
216A TYR* 3.4 39.2 + + + -
239A THR* 1.4 70.4 - - - +
241A GLU* 1.4 53.8 + - - +
243A TYR* 3.0 6.4 + - + +
244A ARG* 2.8 72.8 + - + +
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Residues in contact with GLU 241 (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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60A ARG* 3.1 55.1 + - + +
63A GLN* 4.8 0.9 + - - +
65A GLY* 3.4 41.7 + - - +
66A LEU* 3.3 13.3 + - + +
187A TYR* 4.8 0.9 + - - -
239A THR* 3.3 0.8 - - - -
240A TYR* 1.4 79.3 - - - +
242A ASP* 1.3 55.0 + - - +
244A ARG* 3.9 18.7 + - - +
245A TRP* 3.1 29.3 + - - +
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Residues in contact with ASP 242 (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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66A LEU* 3.4 15.4 - - - +
67A SER* 2.4 47.7 + - - -
68A VAL 4.7 0.5 + - - -
161A LEU* 3.3 30.1 - - + +
164A ARG* 5.5 2.9 + - - -
234A LEU* 5.5 2.0 - - - +
237A SER 3.9 1.6 - - - +
238A PHE* 3.6 13.1 - - + -
239A THR* 3.1 34.6 + - - +
240A TYR 3.1 0.4 - - - -
241A GLU* 1.3 74.3 - - - +
243A TYR* 1.3 59.4 + - - +
245A TRP* 3.4 2.8 + - - +
246A ALA* 3.0 22.3 + - - +
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Residues in contact with TYR 243 (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 ILE* 3.5 17.8 - - + +
157A ALA* 5.0 2.7 - - + -
158A PHE* 3.6 28.7 - + - -
161A LEU* 4.4 4.0 - - + -
212A THR* 3.6 24.5 - - + -
215A GLN* 2.6 54.4 + - + +
216A TYR* 3.7 27.4 - + + -
219A PHE* 4.9 1.2 - + - -
238A PHE* 3.8 22.7 - + + -
239A THR 3.3 1.0 + - - -
240A TYR* 3.0 8.5 + + - +
242A ASP* 1.3 77.2 - - - +
244A ARG* 1.4 59.7 + - - +
246A ALA* 3.3 4.2 + - + +
247A VAL* 3.0 51.6 + - + +
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Residues in contact with ARG 244 (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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57A GLU* 5.0 4.9 + - - -
60A ARG* 3.9 20.9 - - - +
186A LEU* 3.0 46.7 + - + -
187A TYR* 3.5 45.6 + - + +
212A THR* 4.9 2.7 - - - -
240A TYR* 2.8 50.6 + - + +
241A GLU* 3.9 27.0 + - - +
243A TYR* 1.4 70.7 - - - +
245A TRP* 1.3 61.5 + - - +
247A VAL* 3.7 7.8 - - - +
248A SER* 3.0 31.0 + - - -
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Residues in contact with TRP 245 (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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66A LEU* 3.7 16.6 - - + -
160A LEU* 3.7 37.0 - - + -
161A LEU* 4.1 12.1 - - + -
164A ARG* 3.2 47.9 - - + +
175A ILE* 4.1 2.9 - - + -
178A LEU* 3.7 22.7 - - + -
179A PRO 2.7 23.0 + - - -
180A SER* 3.5 27.4 - - - +
182A TYR* 3.7 11.7 - + - -
187A TYR* 3.3 13.2 + - - +
241A GLU 3.1 20.4 + - - +
242A ASP 3.7 5.8 - - - +
243A TYR 3.3 0.2 - - - -
244A ARG* 1.3 77.7 - - - +
246A ALA* 1.4 66.9 + - - +
249A SER* 2.8 51.5 + - - -
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Residues in contact with ALA 246 (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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157A ALA* 3.5 32.5 - - + +
160A LEU* 4.2 1.6 - - - +
161A LEU* 3.6 18.6 - - + -
242A ASP 3.0 17.5 + - - +
243A TYR* 3.7 5.2 - - + +
245A TRP* 1.4 83.6 - - + +
247A VAL* 1.3 60.0 + - - +
249A SER* 3.4 4.5 + - - -
250A VAL* 3.0 32.6 + - - +
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Residues in contact with VAL 247 (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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153A ASN 6.2 0.2 - - - -
154A ILE* 4.8 6.7 - - + -
157A ALA* 3.9 14.8 - - + -
186A LEU* 3.9 20.4 - - + -
212A THR* 4.0 14.6 - - + +
215A GLN* 4.5 4.0 - - - +
243A TYR* 3.0 56.6 + - + +
244A ARG* 3.7 5.8 - - - +
246A ALA* 1.3 73.5 - - - +
248A SER* 1.4 59.6 + - - +
250A VAL* 3.4 3.8 + - - +
251A MSE 2.9 41.2 + - + +
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Residues in contact with SER 248 (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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182A TYR* 3.5 24.5 - - - -
184A THR* 3.1 24.2 + - - -
186A LEU* 3.5 11.8 - - - +
187A TYR* 3.5 9.2 - - - -
244A ARG 3.0 23.6 + - - -
247A VAL* 1.4 73.2 - - - +
249A SER* 1.3 54.3 + - - +
251A MSE 3.7 8.6 - - - -
252A THR* 2.8 41.5 + - - +
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 3.5 20.2 - - - -
178A LEU* 4.6 3.8 - - - +
182A TYR* 2.6 31.6 + - - -
245A TRP* 2.8 38.0 + - - -
246A ALA 3.4 5.8 - - - -
248A SER* 1.3 73.9 - - - +
250A VAL* 1.3 62.5 + - - +
252A THR* 4.0 0.7 - - - -
253A ARG* 3.2 33.7 + - - +
269A LEU* 4.4 2.9 - - - +
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Residues in contact with VAL 250 (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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153A ASN* 3.7 26.5 - - + +
156A LEU* 4.0 19.1 - - + +
157A ALA* 3.6 26.0 - - - +
160A LEU* 4.6 2.5 - - + -
246A ALA 3.0 20.3 + - - +
247A VAL* 3.8 6.1 - - - +
248A SER 3.3 0.2 - - - -
249A SER* 1.3 74.8 - - - +
251A MSE 1.3 59.5 + - - +
254A GLN* 2.7 58.9 + - + +
269A LEU* 4.2 15.9 - - + -
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Residues in contact with MSE 251 (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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184A THR* 3.9 12.3 - - - -
186A LEU* 4.3 9.0 - - + -
208A GLN* 3.6 32.5 - - + +
212A THR* 5.3 1.8 - - - +
247A VAL* 2.9 46.2 + - + +
248A SER* 3.5 9.6 - - - +
250A VAL* 1.3 73.5 - - - +
252A THR* 1.4 63.9 + - + +
253A ARG 3.6 0.2 + - - -
254A GLN* 4.1 10.5 - - - +
315A ARG* 5.6 2.1 + - - -
322A ILE 3.8 9.6 - - - +
323A HIS* 3.1 35.0 - - + +
324A SER* 4.5 3.3 + - - -
505A UNX 3.3 25.4 - - - -
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Residues in contact with THR 252 (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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182A TYR* 3.6 20.9 - - + -
184A THR* 3.5 28.7 - - + -
248A SER 2.8 26.2 + - - +
249A SER 3.5 0.3 + - - -
251A MSE 1.4 75.6 - - - +
253A ARG* 1.3 71.0 + - - +
312A TYR* 5.0 3.8 - - - -
323A HIS 3.5 8.7 - - - +
324A SER* 3.7 13.5 + - - +
1000A SAM 3.4 44.9 + - - +
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Residues in contact with ARG 253 (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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74A ARG* 4.3 1.2 - - - +
174A TYR* 4.4 2.0 - - - -
177A THR 6.0 0.2 - - - -
178A LEU* 3.4 29.7 - - - +
179A PRO* 3.5 15.5 - - - +
182A TYR* 4.3 9.0 - - - -
249A SER* 3.2 20.9 + - - +
252A THR* 1.3 93.5 - - - +
254A GLN* 1.3 60.3 + - - +
255A ASN* 2.9 24.1 + - - -
268A ALA 4.4 1.6 - - - +
269A LEU* 4.4 10.3 - - + +
274A ASP* 2.9 59.9 + - - +
275A MSE 3.6 13.9 - - - -
1000A SAM 2.7 51.8 + - + +
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Residues in contact with GLN 254 (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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153A ASN* 3.8 2.3 - - - +
156A LEU* 5.1 0.7 - - + -
250A VAL* 2.7 45.8 + - + +
251A MSE 4.3 9.8 + - - +
253A ARG* 1.3 73.4 - - - +
255A ASN* 1.3 62.7 + - - +
267A LEU* 3.7 39.0 - - + +
268A ALA 3.5 9.6 - - - +
269A LEU* 4.2 4.7 - - + +
315A ARG* 5.1 9.2 + - - -
505A UNX 3.3 21.5 - - - -
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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
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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