Contacts of the helix formed by residues 240 - 255 (chain A) in PDB entry 1LDI
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 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ALA* 3.9 4.5 - - + -
152A GLU* 4.0 7.2 - - + +
156A THR* 3.4 14.8 - - - +
202A MET* 3.6 39.0 - - - +
203A ASN 3.9 3.1 - - - +
204A PRO* 3.9 12.3 - - + -
235A VAL 3.0 23.6 - - - +
236A PRO* 3.1 27.1 - - + +
237A LEU 4.0 0.9 - - - -
238A PHE 3.6 2.2 - - - -
239A GLY* 1.3 79.1 - - - +
241A ILE* 1.3 57.4 + - - +
243A GLY 3.4 0.2 + - - -
244A ALA* 2.8 32.4 + - - +
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Residues in contact with ILE 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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69A PRO* 5.6 1.6 - - + -
70A ALA* 4.1 11.4 - - - +
73A ILE* 3.8 44.6 - - + -
204A PRO* 3.9 16.4 - - + -
237A LEU* 3.3 24.2 - - + +
238A PHE* 3.2 22.1 + - + +
240A PRO* 1.3 75.4 - - - +
242A VAL* 1.3 66.3 + - + +
244A ALA* 3.4 2.1 + - - +
245A ILE* 3.2 28.2 + - + +
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Residues in contact with VAL 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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149A PHE* 4.0 17.0 - - + -
153A MET* 4.0 23.1 - - + -
238A PHE* 3.0 20.4 + - + +
239A GLY 3.8 3.1 - - - +
241A ILE* 1.3 76.1 - - + +
243A GLY* 1.3 64.9 - - - +
245A ILE* 3.1 13.4 + - - +
246A VAL* 3.0 28.6 + - + +
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Residues in contact with GLY 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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153A MET* 3.3 30.6 - - - +
156A THR* 4.5 0.4 - - - -
157A ALA* 3.0 15.2 - - - +
239A GLY 3.1 9.7 + - - -
240A PRO 3.8 2.2 - - - -
242A VAL* 1.3 77.4 - - - +
244A ALA* 1.3 55.0 + - - +
246A VAL* 3.1 6.2 + - - -
247A GLY 2.7 31.5 + - - -
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Residues in contact with ALA 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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70A ALA* 3.4 35.9 - - + +
71A VAL* 5.8 0.7 - - + -
74A ALA* 3.7 6.4 - - + +
156A THR* 4.0 9.9 - - + +
160A MET* 3.2 26.5 - - + +
240A PRO 2.8 21.5 + - - +
241A ILE 3.8 3.8 - - - +
242A VAL 3.3 0.2 - - - -
243A GLY* 1.3 71.6 - - - +
245A ILE* 1.3 57.4 + - - +
248A ALA* 3.0 25.3 + - - +
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.5 8.7 - - + -
74A ALA* 4.7 6.3 - - + -
77A LEU* 3.7 26.7 - - + -
78A PHE* 3.5 27.8 - - + -
241A ILE* 3.2 26.9 - - + +
242A VAL* 3.1 10.7 + - - +
244A ALA* 1.3 76.9 - - + +
246A VAL* 1.3 61.0 + - + +
248A ALA* 3.4 2.2 + - - +
249A PHE* 2.9 29.8 + - + +
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Residues in contact with VAL 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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153A MET* 5.4 9.2 - - + -
157A ALA* 4.3 10.8 - - + -
242A VAL* 3.0 29.2 + - + +
243A GLY* 3.5 11.4 - - - +
245A ILE* 1.3 77.9 - - + +
247A GLY* 1.3 59.6 + - - +
249A PHE* 3.6 7.3 - - - +
250A ALA* 2.8 31.4 + - + +
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Residues in contact with GLY 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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157A ALA* 3.2 31.9 - - - -
160A MET* 4.5 0.2 - - - -
161A GLY* 4.1 9.4 - - - -
243A GLY 2.7 17.7 + - - -
244A ALA 4.0 0.4 - - - -
246A VAL* 1.3 71.9 - - - +
248A ALA* 1.3 64.2 + - - +
250A ALA* 3.1 8.4 + - - +
251A TYR* 3.0 23.6 + - - +
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Residues in contact with ALA 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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74A ALA* 4.2 7.2 - - + +
78A PHE* 3.8 26.7 - - + -
160A MET* 3.8 13.6 - - + +
164A LEU* 3.9 19.9 - - + +
244A ALA 3.0 19.6 + - - +
245A ILE 3.8 3.6 - - - +
247A GLY* 1.3 74.7 - - - +
249A PHE* 1.3 64.1 + - - +
251A TYR* 3.6 2.3 + - - +
252A ARG* 3.4 26.8 + - - +
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Residues in contact with PHE 249 (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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78A PHE* 3.6 30.2 - + + -
245A ILE* 2.9 20.5 + - + +
246A VAL* 3.6 7.4 - - - +
248A ALA* 1.3 76.5 - - - +
250A ALA* 1.3 66.0 + - - +
252A ARG* 3.1 6.8 + - + +
253A LYS* 3.0 63.3 + - + +
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Residues in contact with ALA 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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246A VAL* 2.8 22.4 + - + +
247A GLY* 3.1 8.5 + - - +
249A PHE* 1.3 81.5 - - - +
251A TYR* 1.3 57.0 + - - +
253A LYS* 4.7 3.4 - - - -
254A LEU* 2.9 50.1 + - + +
255A ILE* 5.1 0.2 - - - +
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Residues in contact with TYR 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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161A GLY* 3.6 23.1 - - - +
164A LEU* 3.8 28.3 - - + -
165A ALA* 3.5 26.9 - - + -
168A ASP* 2.9 37.9 + - + +
171A ASN* 3.0 20.5 + - - +
247A GLY 3.0 15.5 + - - +
248A ALA 3.9 4.5 - - - +
249A PHE 3.2 0.2 - - - -
250A ALA* 1.3 76.8 - - - +
252A ARG* 1.3 67.7 + - - +
255A ILE* 2.9 46.8 + - + +
256A GLY* 2.7 37.6 + - - -
259A LEU* 3.7 2.2 - - + +
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Residues in contact with ARG 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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78A PHE* 2.8 50.8 + - + +
79A ALA* 3.7 16.2 - - - +
164A LEU* 4.3 24.9 - - - +
168A ASP* 5.6 1.0 + - - -
248A ALA 3.4 14.3 + - - +
249A PHE* 3.1 9.7 + - + +
251A TYR* 1.3 93.3 - - + +
253A LYS* 1.3 67.5 + - + +
256A GLY* 3.9 5.1 - - - +
257A ARG* 3.0 26.2 + - - +
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Residues in contact with LYS 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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249A PHE* 3.0 60.6 + - + +
250A ALA* 4.0 2.9 - - - +
252A ARG* 1.3 84.6 + - - +
254A LEU* 1.3 72.6 + - + +
257A ARG* 3.1 24.6 - - - +
258A HIS* 3.7 7.3 + - - -
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Residues in contact with LEU 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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250A ALA* 2.9 31.6 + - + +
253A LYS* 1.3 78.3 - - + +
255A ILE* 1.3 73.2 + - + +
258A HIS* 3.6 18.6 + - - +
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Residues in contact with ILE 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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171A ASN* 3.6 19.1 - - - +
251A TYR* 2.9 45.1 + - + +
254A LEU* 1.3 95.5 - - + +
256A GLY* 1.3 66.2 + - - +
257A ARG 3.2 1.6 - - - -
258A HIS* 3.0 16.0 + - - +
259A LEU* 3.3 16.8 - - + +
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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