Contacts of the helix formed by residues 249 - 262 (chain A) in PDB entry 1LTM
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PHE* 4.4 5.6 - - + -
137A TYR* 3.3 47.3 - - + +
223A TYR* 3.6 41.0 - - + +
247A TRP 3.7 2.2 - - - +
248A ASP* 1.3 88.0 - - - +
250A VAL* 1.3 57.0 + - + +
252A ALA* 3.7 3.2 - - + +
253A ILE* 3.0 36.6 + - - +
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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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137A TYR* 4.2 23.6 - - + -
140A ALA* 4.1 14.1 - - + -
143A ARG* 3.6 27.1 - - - +
238A PHE* 3.4 6.5 - - + +
239A SER* 3.6 25.1 - - - +
248A ASP* 2.9 10.7 + - - +
249A PRO* 1.3 75.0 - - + +
251A ASP* 1.3 66.4 + - - +
253A ILE* 3.3 8.3 + - - +
254A GLY 3.1 18.0 + - - -
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Residues in contact with ASP 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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236A VAL 3.9 12.2 - - - +
238A PHE* 2.9 21.2 + - - -
239A SER* 2.9 8.5 + - - -
241A ASP* 4.4 0.9 - - - +
243A HIS 3.3 0.4 - - - +
244A ILE* 5.0 0.9 - - + -
245A ASN* 2.9 47.6 + - - +
246A LEU* 5.4 0.9 - - - -
248A ASP* 3.0 16.2 + - - +
250A VAL* 1.3 76.1 - - - +
252A ALA* 1.3 54.2 + - - +
254A GLY* 3.3 1.6 + - - -
255A SER* 2.7 39.0 + - - +
400A NA 2.5 31.2 - - - -
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Residues in contact with ALA 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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159A ILE* 4.6 5.6 - - + -
223A TYR* 3.6 29.8 - - + -
224A GLY* 4.5 6.5 - - - +
245A ASN 4.4 1.2 + - - -
246A LEU* 4.0 14.8 - - + +
248A ASP 2.9 17.2 + - - +
249A PRO 3.7 5.4 - - - +
250A VAL 3.3 0.2 - - - -
251A ASP* 1.3 76.6 - - - +
253A ILE* 1.3 56.4 + - - +
255A SER* 3.7 5.8 - - - -
256A VAL* 2.9 37.3 + - - +
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Residues in contact with ILE 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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133A PHE* 3.9 14.8 - - + -
137A TYR* 3.6 32.3 - - + -
140A ALA* 3.9 30.3 - - + +
141A LEU* 3.9 23.6 - - + -
144A ALA* 4.0 10.1 - - + -
155A ILE* 4.0 16.0 - - + +
159A ILE* 4.0 16.8 - - + -
238A PHE* 4.7 0.7 - - + -
249A PRO 3.0 26.6 + - - +
250A VAL* 3.6 5.4 - - - +
252A ALA* 1.3 76.1 - - - +
254A GLY* 1.3 63.0 + - - +
256A VAL* 3.4 2.8 + - - +
257A ALA* 3.0 22.2 + - - +
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Residues in contact with GLY 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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148A TYR* 3.8 2.6 - - - -
236A VAL* 3.6 8.5 - - - +
238A PHE* 3.5 37.0 - - - -
250A VAL 3.1 11.1 + - - -
253A ILE* 1.3 77.4 - - - +
255A SER* 1.3 57.4 + - - +
257A ALA* 3.3 7.6 + - - +
258A ASN* 2.9 29.6 + - - +
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Residues in contact with SER 255 (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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226A PHE* 3.4 19.3 - - - -
234A TYR 3.9 5.1 - - - +
235A ALA* 3.3 17.7 - - - +
236A VAL* 3.0 28.5 + - - +
244A ILE* 4.7 1.2 - - - +
246A LEU* 4.9 4.5 - - - +
251A ASP* 2.7 22.7 + - - +
252A ALA* 3.7 7.2 - - - -
254A GLY* 1.3 73.5 - - - +
256A VAL* 1.3 60.1 + - - +
258A ASN* 3.4 2.3 + - - +
259A TYR* 2.9 29.1 + - - +
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Residues in contact with VAL 256 (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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155A ILE* 4.2 20.2 - - + -
158A ILE* 4.0 28.5 - - + -
159A ILE* 4.4 11.9 - - + -
224A GLY* 4.4 6.5 - - - -
226A PHE* 4.2 7.0 - - + -
252A ALA* 2.9 22.9 + - - +
253A ILE 3.8 4.0 - - - +
255A SER* 1.3 74.8 - - - +
257A ALA* 1.3 62.8 + - - +
259A TYR* 3.3 6.6 + - - +
260A PHE* 3.0 42.0 + - + -
338A TYR* 3.6 22.0 - - + +
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Residues in contact with ALA 257 (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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144A ALA* 3.8 8.7 - - + -
148A TYR* 3.5 26.8 - - + +
150A VAL* 3.4 21.5 - - + +
155A ILE* 3.8 17.9 - - + +
253A ILE 3.0 14.3 + - - +
254A GLY 3.5 7.9 - - - +
255A SER 3.3 0.2 - - - -
256A VAL* 1.3 77.3 - - - +
258A ASN* 1.3 57.4 + - - +
260A PHE* 3.2 2.0 + - - -
261A LYS* 3.0 25.8 + - - +
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Residues in contact with ASN 258 (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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148A TYR* 3.2 34.0 - - + +
233A GLN 4.6 2.8 + - - -
234A TYR* 2.8 41.8 + - - +
236A VAL* 3.8 14.1 - - + +
254A GLY 2.9 16.3 + - - +
255A SER 3.8 0.7 - - - +
256A VAL 3.3 0.4 - - - -
257A ALA* 1.3 72.9 - - - +
259A TYR* 1.3 60.8 + - - +
261A LYS* 4.5 2.8 - - - +
262A ALA* 2.8 35.7 + - - +
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Residues in contact with TYR 259 (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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226A PHE* 4.1 18.8 - + + -
230A SER* 3.7 20.2 - - - -
234A TYR* 3.5 31.1 - + + +
255A SER 2.9 14.3 + - - +
256A VAL* 3.4 11.0 - - - +
258A ASN* 1.3 75.5 - - - +
260A PHE* 1.3 63.2 - + - +
262A ALA* 3.4 0.5 + - - +
263A HIS* 2.8 63.7 + + + -
334A THR 5.4 1.3 - - - -
337A ARG* 2.6 32.5 + - + -
338A TYR* 3.6 23.6 - + + -
401A BCN 3.5 28.0 + - - -
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Residues in contact with PHE 260 (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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150A VAL* 3.6 18.2 - - + -
154A ILE* 3.5 23.8 - - + -
158A ILE* 3.7 37.2 - - + -
256A VAL* 3.0 28.8 + - + +
257A ALA 3.5 7.9 - - - +
258A ASN 3.2 0.2 - - - -
259A TYR* 1.3 80.8 - + - +
261A LYS* 1.3 65.6 + - - +
263A HIS* 3.1 9.6 + - - -
264A GLY 3.3 0.7 + - - -
265A TRP* 3.0 45.0 + + + +
334A THR* 3.7 12.9 - - + +
335A ILE* 3.8 35.9 - - + -
338A TYR* 3.9 15.9 - + + -
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Residues in contact with LYS 261 (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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147A VAL 4.3 11.9 + - - -
148A TYR* 3.9 43.8 + - + +
150A VAL* 4.2 0.8 - - - +
257A ALA 3.0 15.5 + - - +
258A ASN* 3.9 5.2 - - - +
260A PHE* 1.3 75.7 - - - +
262A ALA* 1.3 59.7 + - - +
264A GLY* 2.9 21.1 + - - -
265A TRP* 3.9 15.2 + - - +
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Residues in contact with ALA 262 (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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234A TYR* 3.5 33.7 - - + -
258A ASN* 2.8 22.6 + - - +
259A TYR 3.6 2.5 - - - +
261A LYS* 1.3 77.8 - - - +
263A HIS* 1.3 59.6 + - - +
264A GLY 3.4 2.8 + - - -
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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