Contacts of the helix formed by residues 248 - 267 (chain A) in PDB entry 4WLE
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLY* 3.4 39.5 - - - -
36A ILE* 4.0 12.7 - - + +
39A PRO* 4.2 0.4 - - - +
241A LYS* 3.2 10.5 + - - +
245A GLY* 6.4 0.2 - - - -
246A SER* 3.2 15.2 + - - +
247A ALA* 1.3 76.2 - - - +
249A LEU* 1.3 76.5 + - - +
250A SER 3.5 1.1 - - - -
251A MET* 3.5 2.2 + - - +
252A ALA* 2.9 30.4 + - - +
38B GLN* 4.2 6.4 + - - -
67B ASP* 2.9 10.5 + - - -
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Residues in contact with LEU 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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39A PRO* 4.1 23.3 - - + -
248A THR* 1.3 86.1 + - - +
250A SER* 1.3 61.0 + - - +
252A ALA* 3.4 6.3 + - - +
253A TYR* 3.0 21.5 + - - +
38B GLN* 3.7 53.6 - - + +
39B PRO* 4.4 1.8 - - + -
42B LEU* 3.6 20.7 - - + +
64B VAL* 4.0 11.2 - - + +
67B ASP* 3.1 10.8 + - + +
68B LEU* 3.6 40.8 - - + -
71B ILE* 4.4 0.2 - - - -
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Residues in contact with SER 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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172A LEU* 3.5 20.7 - - - +
176A ARG* 4.8 0.9 + - - -
247A ALA* 3.7 12.3 - - - +
249A LEU* 1.3 71.3 - - - +
251A MET* 1.3 61.1 + - - +
253A TYR* 3.3 3.8 + - - +
254A ALA* 2.9 28.6 + - - +
67B ASP* 2.6 46.4 + - - -
70B HIS* 4.5 6.6 + - - +
71B ILE* 3.8 23.7 - - - +
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Residues in contact with MET 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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36A ILE* 4.0 28.1 - - + +
140A ILE* 3.8 23.3 - - + +
169A VAL* 3.8 31.6 - - + +
172A LEU* 3.9 18.8 - - + -
247A ALA* 3.7 20.4 - - + +
248A THR 3.5 4.8 + - - +
249A LEU 3.3 0.4 - - - -
250A SER* 1.3 77.7 + - - +
252A ALA* 1.3 61.3 + - - +
254A ALA* 4.3 5.2 - - + -
255A GLY* 2.8 33.5 + - - +
401A CIT 3.3 35.9 - - + +
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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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36A ILE* 4.1 5.9 - - - +
39A PRO* 3.7 16.2 - - + +
40A LEU* 3.4 40.6 - - - +
43A LEU* 3.6 6.5 - - + +
248A THR 2.9 19.5 + - - +
249A LEU 3.5 6.5 - - - +
250A SER 3.3 0.2 - - - -
251A MET* 1.3 72.6 - - - +
253A TYR* 1.3 64.5 + - - +
255A GLY 3.5 0.2 + - - -
256A ALA* 2.9 26.7 + - - +
42B LEU* 4.4 0.2 - - + -
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Residues in contact with TYR 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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43A LEU* 3.7 10.9 - - + +
175A VAL* 3.8 18.4 - - + -
249A LEU 3.0 15.0 + - - +
250A SER 3.5 7.6 - - - +
251A MET 3.3 0.2 - - - -
252A ALA* 1.3 77.5 - - - +
254A ALA* 1.3 61.8 + - - +
256A ALA* 3.3 2.4 + - - +
257A ARG* 2.9 36.7 + - + +
42B LEU* 4.5 3.8 - - + -
46B ASN* 3.6 28.0 - - + -
71B ILE* 3.8 28.9 - - + -
72B GLU* 2.7 47.3 + - + +
73B THR* 4.8 8.0 - - + +
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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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171A THR* 3.5 22.8 - - + +
172A LEU* 3.5 40.8 - - + +
175A VAL* 4.3 4.3 - - + -
250A SER 2.9 17.4 + - - +
251A MET* 3.8 7.2 - - + +
253A TYR* 1.3 78.7 - - - +
255A GLY* 1.3 65.0 + - - +
257A ARG* 3.3 2.4 + - - +
258A PHE* 3.0 18.7 + - - +
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Residues in contact with GLY 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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40A LEU* 4.0 11.0 - - - -
97A VAL* 5.3 2.1 - - - +
140A ILE* 4.6 9.0 - - - -
169A VAL* 4.6 9.0 - - - -
251A MET* 2.8 31.9 + - - +
252A ALA 3.9 0.9 - - - -
254A ALA* 1.3 73.8 - - - +
256A ALA* 1.3 59.3 + - - +
258A PHE* 3.3 3.6 + - - +
259A VAL* 3.1 27.8 + - - +
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Residues in contact with ALA 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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40A LEU* 3.6 11.0 - - + +
43A LEU* 3.9 24.2 - - + -
44A LEU* 4.7 3.1 - - + -
252A ALA 2.9 19.2 + - - +
253A TYR 3.6 3.8 - - - +
255A GLY* 1.3 72.1 - - - +
257A ARG* 1.3 65.1 + - - +
259A VAL* 3.3 6.3 + - - +
260A PHE* 2.9 51.1 + - + -
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Residues in contact with ARG 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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171A THR* 3.9 15.4 - - + +
174A ILE* 4.0 19.2 - - - +
175A VAL* 4.1 6.8 - - - +
178A ASN* 3.9 7.7 - - - +
193A ASN* 4.6 11.5 + - - -
253A TYR* 2.9 23.6 + - + +
254A ALA* 3.3 9.2 + - - +
256A ALA* 1.3 75.9 - - - +
258A PHE* 1.3 57.3 + - - +
260A PHE* 3.3 11.1 + - - +
261A SER* 2.9 32.7 + - - +
273A VAL 5.0 3.0 + - - -
274A GLU* 3.0 36.1 + - - +
72B GLU* 2.8 49.2 + - - -
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Residues in contact with PHE 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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138A CYS* 3.7 12.3 - - + -
167A PHE* 3.6 43.3 - + + -
169A VAL* 4.2 18.8 - - + -
171A THR* 3.4 26.0 - - - +
254A ALA 3.0 9.1 + - - +
255A GLY 3.7 7.6 - - - +
257A ARG* 1.3 78.1 - - - +
259A VAL* 1.3 58.9 + - + +
261A SER* 3.3 5.2 + - - -
262A LEU* 3.0 60.4 + - + +
274A GLU* 3.8 31.6 - - + -
275A CYS 4.2 1.3 - - - -
276A SER* 3.8 17.3 - - - -
294A LEU* 4.9 2.2 - - + -
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Residues in contact with VAL 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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27A VAL* 4.2 20.4 - - + -
40A LEU* 5.6 0.4 - - + -
44A LEU* 3.9 25.8 - - + -
50A VAL* 5.6 0.9 - - + -
95A VAL* 4.2 12.1 - - + -
97A VAL* 3.4 33.7 - - + -
138A CYS* 4.8 5.8 - - + -
255A GLY 3.1 15.8 + - - +
256A ALA 3.7 6.5 - - - +
258A PHE* 1.3 77.4 - - + +
260A PHE* 1.3 60.9 + - + +
262A LEU* 3.2 9.4 + - - +
263A VAL* 2.9 35.7 + - + +
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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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43A LEU* 3.7 15.5 - - + -
44A LEU* 3.9 19.3 - - + -
47A SER* 3.3 33.9 - - - -
49A LEU* 3.9 26.6 - - + +
50A VAL* 4.5 4.7 - - + -
256A ALA* 2.9 40.5 + - + +
257A ARG* 3.7 8.1 - - - +
259A VAL* 1.3 81.0 - - + +
261A SER* 1.3 57.8 + - - +
263A VAL* 3.8 3.3 - - + +
264A ASP* 2.9 37.4 + - - +
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Residues in contact with SER 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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257A ARG* 2.9 13.3 + - - +
258A PHE 3.6 7.9 - - - -
259A VAL 3.3 0.2 - - - -
260A PHE* 1.3 74.3 - - - +
262A LEU* 1.3 58.3 + - - +
264A ASP* 3.4 5.8 + - - +
265A ALA* 3.0 25.5 + - - +
272A VAL* 3.5 25.0 - - - +
274A GLU* 2.6 42.9 + - - +
294A LEU* 4.3 3.8 - - - -
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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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95A VAL* 4.4 12.3 - - + -
136A MET* 4.0 27.1 - - + -
138A CYS* 3.3 34.1 - - - -
167A PHE* 4.0 21.5 - - + -
258A PHE* 3.0 29.2 + - + +
259A VAL* 3.4 9.4 - - - +
261A SER* 1.3 76.7 - - - +
263A VAL* 1.3 56.9 + - - +
265A ALA* 3.4 4.1 + - + +
266A MET* 2.9 34.7 + - - +
294A LEU* 3.5 27.8 - - + -
298A GLY* 5.6 2.5 - - - -
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Residues in contact with VAL 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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24A ASN 5.6 0.4 - - - +
25A ALA* 3.6 35.0 - - + +
27A VAL* 5.1 0.9 - - + -
49A LEU* 4.1 25.1 - - + +
50A VAL* 6.0 1.1 - - + -
95A VAL* 4.3 12.8 - - + -
259A VAL* 2.9 32.7 + - + +
260A PHE* 3.9 7.4 - - + +
262A LEU* 1.3 72.6 - - - +
264A ASP* 1.3 61.1 + - - +
266A MET* 3.3 8.4 + - + +
267A ASN* 2.9 47.2 + - - +
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Residues in contact with ASP 264 (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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49A LEU* 3.7 25.4 - - - +
260A PHE* 2.9 23.7 + - - +
261A SER* 3.7 7.2 - - - +
263A VAL* 1.3 76.5 - - - +
265A ALA* 1.3 61.9 + - - +
267A ASN* 3.2 15.0 + - - +
268A GLY 3.2 0.7 + - - -
269A LYS* 3.0 54.1 + - + +
272A VAL* 4.3 4.9 - - + -
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Residues in contact with ALA 265 (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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261A SER 3.0 17.9 + - - +
262A LEU* 3.6 4.7 - - - +
264A ASP* 1.3 75.1 - - - +
266A MET* 1.3 59.1 + - - +
268A GLY* 3.0 19.1 + - - -
269A LYS 4.1 11.5 - - - +
272A VAL* 4.3 6.0 - - + +
294A LEU* 3.6 36.8 - - + +
295A GLY* 3.5 24.0 - - - +
296A LYS* 3.6 2.8 + - - -
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Residues in contact with MET 266 (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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25A ALA* 6.1 1.6 - - + -
94A ASP* 3.8 35.0 - - + +
95A VAL* 4.4 12.8 - - - -
136A MET* 3.9 36.8 - - + -
262A LEU 2.9 21.6 + - - +
263A VAL* 3.6 9.2 - - + +
265A ALA* 1.3 76.0 - - - +
267A ASN* 1.3 63.9 + - - +
268A GLY 3.2 0.9 + - - -
295A GLY 4.4 3.1 - - - +
296A LYS* 3.9 36.7 - - - +
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Residues in contact with ASN 267 (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 ASN* 4.4 21.1 + - - +
25A ALA 6.0 0.4 - - - +
49A LEU* 4.4 10.4 - - - +
263A VAL* 2.9 37.1 + - - +
264A ASP* 3.2 9.2 + - - +
266A MET* 1.3 80.9 + - - +
268A GLY* 1.3 58.7 + - - +
269A LYS 3.6 1.5 + - - +
296A LYS* 5.1 2.0 - - - -
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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