Contacts of the helix formed by residues 247 - 263 (chain A) in PDB entry 4ND1
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 TYR 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.6 53.1 + - + -
32A ILE* 3.6 22.8 - - + +
35A ASN* 3.2 30.5 + - - -
243A LEU* 4.0 21.8 - - + -
245A THR 3.4 14.6 - - - +
246A ALA* 1.3 75.4 - - - +
248A PHE* 1.3 94.2 + + - +
249A ALA 3.5 1.1 - - - -
250A PRO* 3.5 4.0 - - - +
251A ALA* 3.3 24.1 + - - +
401A NAD 4.7 0.4 - - - +
31B GLN* 5.5 4.2 + - - -
62B LYS* 3.5 21.1 + - - -
65B ASP* 2.7 15.1 + - - -
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Residues in contact with PHE 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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35A ASN* 3.5 18.8 - - - +
247A TYR* 1.3 111.3 - + - +
249A ALA* 1.3 61.6 + - - +
252A ALA* 3.2 9.5 + - - +
34B GLY* 3.9 27.8 - - - -
35B ASN* 4.1 11.2 - - - -
38B TYR* 2.7 63.4 + + + -
62B LYS* 4.1 16.2 - - + -
65B ASP* 2.9 29.8 + - + -
66B ILE* 3.5 28.5 - - + +
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Residues in contact with ALA 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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167A LEU* 3.6 18.6 - - + -
171A ARG* 5.6 0.2 - - - +
248A PHE* 1.3 71.2 - - - +
250A PRO* 1.3 65.8 - - + +
252A ALA 3.2 1.2 + - - -
253A ALA* 2.9 25.5 + - - +
65B ASP* 2.9 30.6 + - - +
68B HIS* 3.8 14.4 - - + +
69B SER* 3.8 15.9 - - - +
72B MET* 3.4 13.3 - - + +
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Residues in contact with PRO 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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32A ILE* 4.0 17.9 - - + -
138A ILE* 4.3 1.6 - - - +
163A MET* 3.6 30.3 - - + +
167A LEU* 3.8 11.7 - - + -
246A ALA* 3.5 25.4 - - + +
247A TYR 3.5 11.9 - - - +
249A ALA* 1.3 94.5 - - + +
251A ALA* 1.3 59.2 + - - +
253A ALA* 3.5 2.4 + - + -
254A ALA* 3.2 20.3 + - - +
401A NAD 3.7 20.9 - - + -
65B ASP* 3.7 5.4 - - - +
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Residues in contact with ALA 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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32A ILE* 3.7 8.4 - - + +
35A ASN* 3.5 27.1 - - + -
36A ILE* 3.6 24.1 - - + +
39A ILE* 5.7 0.4 - - + -
247A TYR 3.3 19.0 + - - +
248A PHE 3.7 2.7 - - - +
249A ALA 3.2 0.6 - - - -
250A PRO* 1.3 76.0 - - - +
252A ALA* 1.3 66.9 + - - +
254A ALA* 3.3 4.5 + - - +
255A VAL* 3.1 27.3 + - - +
38B TYR* 3.9 2.2 - - - +
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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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39A ILE* 5.6 1.8 - - - -
248A PHE 3.2 10.1 + - - +
249A ALA 3.2 8.2 + - - +
251A ALA* 1.3 79.3 - - - +
253A ALA* 1.3 62.1 - - - +
255A VAL* 3.2 9.9 + - - +
256A LYS* 3.0 26.2 + - - +
38B TYR* 3.8 2.8 + - - +
69B SER* 4.0 6.7 - - - -
72B MET* 3.6 15.9 - - + -
73B PHE* 3.5 34.8 - - + -
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Residues in contact with ALA 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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163A MET* 3.6 27.4 - - + -
166A VAL* 3.5 26.4 - - + +
167A LEU* 4.2 2.0 - - - +
249A ALA 2.9 16.3 + - - +
250A PRO* 3.7 2.2 - - + +
252A ALA* 1.3 77.4 - - - +
254A ALA* 1.3 61.7 + - - +
256A LYS* 3.2 6.0 + - - +
257A MET* 3.1 25.1 + - - +
72B MET* 3.4 13.6 - - + -
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Residues in contact with ALA 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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36A ILE* 3.9 11.9 - - + -
95A ILE* 4.1 11.6 - - + +
136A ILE* 4.1 7.7 - - + +
138A ILE* 3.6 31.9 - - + -
163A MET* 3.9 9.7 - - + +
250A PRO 3.2 5.6 + - - +
251A ALA 3.3 8.3 + - - +
253A ALA* 1.3 77.8 - - - +
255A VAL* 1.3 57.0 + - - +
257A MET* 3.3 8.1 + - - +
258A ALA* 2.9 27.8 + - - +
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Residues in contact with VAL 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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36A ILE* 4.1 18.2 - - + +
39A ILE* 4.1 28.9 - - + -
40A VAL* 3.8 24.2 - - + +
43A ASP* 4.2 5.4 - - - +
45A LEU* 4.3 14.6 - - + -
95A ILE* 5.4 0.4 - - - -
251A ALA 3.1 15.4 + - - +
252A ALA* 3.2 8.3 + - - +
254A ALA* 1.3 73.3 - - - +
256A LYS* 1.3 59.7 + - + +
258A ALA* 3.2 7.4 + - - +
259A GLU* 2.8 44.2 + - - +
73B PHE* 6.1 0.9 - - + -
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Residues in contact with LYS 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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166A VAL* 4.9 9.4 - - + -
252A ALA 3.0 20.6 + - - +
253A ALA* 3.2 9.8 + - - +
255A VAL* 1.3 76.4 - - + +
257A MET* 1.3 63.8 + - + +
259A GLU* 3.1 37.3 + - - +
260A ALA* 3.0 21.1 + - - +
265A LYS* 4.1 11.5 + - - +
269A VAL* 5.7 1.3 - - - +
72B MET* 3.5 41.6 + - + +
73B PHE* 5.4 8.6 - - + +
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Residues in contact with MET 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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134A PHE* 4.4 2.2 - - + -
136A ILE* 3.8 18.8 - - + -
161A CYS* 3.5 32.3 - - - -
162A GLY 4.1 4.0 - - - +
163A MET* 3.6 37.7 - - - -
166A VAL* 4.3 7.9 - - + -
253A ALA 3.1 10.3 + - - +
254A ALA 3.5 7.4 - - - +
256A LYS* 1.3 76.6 - - - +
258A ALA* 1.3 61.4 + - - +
260A ALA* 3.2 16.6 + - - +
261A TYR* 3.3 13.2 + - - +
269A VAL* 3.8 19.7 - - + -
271A CYS* 3.6 26.2 - - + -
293A ILE* 4.2 12.7 - - + +
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Residues in contact with ALA 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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24A ILE* 4.0 27.1 - - + -
45A LEU* 4.3 2.9 - - + -
93A VAL* 4.5 10.1 - - + -
95A ILE* 4.5 4.5 - - + -
136A ILE* 3.8 13.8 - - + +
254A ALA 2.9 14.9 + - - +
255A VAL* 3.5 12.8 - - - +
257A MET* 1.3 73.3 - - - +
259A GLU* 1.3 58.9 + - - +
261A TYR* 3.3 5.8 + - - +
262A LEU* 2.9 35.3 + - - +
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Residues in contact with GLU 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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43A ASP* 4.1 10.7 - - - +
45A LEU* 3.9 30.5 - - + +
255A VAL* 2.8 34.4 + - - +
256A LYS* 3.1 35.3 + - - +
257A MET 3.3 0.2 - - - -
258A ALA* 1.3 72.3 - - - +
260A ALA* 1.3 58.1 + - - +
263A LYS* 2.8 41.0 + - + +
265A LYS* 2.8 29.6 + - - +
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Residues in contact with ALA 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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256A LYS 3.0 10.0 + - - +
257A MET 3.2 10.0 + - - +
259A GLU* 1.3 78.2 - - - +
261A TYR* 1.3 58.0 + - - +
264A ASP* 3.1 6.9 + - - -
265A LYS* 2.9 37.2 + - + +
267A ALA* 4.1 17.7 - - + -
269A VAL* 4.4 7.2 - - + -
293A ILE* 3.6 32.1 - - + +
294A GLY* 3.7 0.3 - - - -
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Residues in contact with TYR 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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92A ASP* 3.6 22.8 + - + -
93A VAL* 3.6 18.8 - - + -
132A ASN 4.3 5.0 + - - -
134A PHE* 3.6 40.5 - + + +
159A LYS* 3.6 21.8 + - - -
257A MET 3.3 6.0 + - - +
258A ALA* 3.7 6.3 - - - +
259A GLU 3.2 0.6 - - - -
260A ALA* 1.3 77.8 - - - +
262A LEU* 1.3 72.6 + - + +
264A ASP* 3.2 13.5 + - - +
293A ILE* 3.7 2.0 - - + +
294A GLY 3.0 23.3 - - - +
295A LYS* 3.2 36.9 + - - +
297A GLY* 3.6 14.4 - - - -
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Residues in contact with LEU 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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22A ARG* 4.2 45.7 + - + -
24A ILE* 3.9 24.5 - - + -
45A LEU* 3.9 39.7 - - + +
92A ASP* 3.8 29.6 - - + -
93A VAL* 3.9 11.9 - - + -
258A ALA 2.9 19.7 + - - +
259A GLU 4.2 1.1 - - - +
261A TYR* 1.3 83.8 - - + +
263A LYS* 1.3 62.0 + - + +
264A ASP* 3.8 1.0 + - - +
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Residues in contact with LYS 263 (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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45A LEU* 4.1 25.8 - - + +
259A GLU* 2.8 23.9 + - + +
262A LEU* 1.3 79.1 - - + +
264A ASP* 1.3 71.1 - - - +
265A LYS* 3.3 25.0 + - + +
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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