Contacts of the helix formed by residues 215 - 233 (chain A) in PDB entry 4LT6
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 ASN 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A VAL* 3.5 3.2 - - - +
214A PRO* 1.3 84.1 - - + +
216A LYS* 1.3 59.6 + - - +
217A GLU* 2.9 24.0 + - - +
218A THR* 3.2 34.6 + - - +
219A PHE* 3.1 27.4 + - - +
256A CYS* 5.3 1.6 - - - +
260A PRO 4.6 13.0 + - - +
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Residues in contact with LYS 216 (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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210A LEU* 3.5 37.6 + - + +
211A HIS* 5.4 6.1 - - - +
213A VAL* 4.0 19.7 + - + +
215A ASN* 1.3 73.7 + - - +
217A GLU* 1.3 66.9 + - - +
219A PHE* 3.7 2.3 - - - +
220A ARG* 3.0 58.1 + - - +
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Residues in contact with GLU 217 (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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215A ASN* 2.9 10.1 + - - +
216A LYS* 1.3 79.2 - - - +
218A THR* 1.3 66.2 + - + +
220A ARG* 3.8 12.9 - - - +
221A LEU* 3.2 23.7 + - + +
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Residues in contact with THR 218 (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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215A ASN* 3.2 36.7 + - - +
217A GLU* 1.3 76.8 - - + +
219A PHE* 1.3 63.7 + - - +
221A LEU* 4.1 4.6 - - - +
222A THR* 2.6 34.8 + - - -
256A CYS* 4.9 2.3 - - - -
260A PRO 5.5 1.0 + - - -
262A ALA 3.8 16.6 + - - +
263A ALA* 5.0 1.8 - - - -
264A ALA* 4.5 8.9 - - + +
267A LEU* 3.7 23.2 - - - +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.0 13.7 - - + -
106A VAL* 5.6 0.2 - - + -
209A ILE* 3.9 20.0 - - + -
210A LEU* 4.0 27.8 - - + -
213A VAL* 3.6 28.0 - - + -
215A ASN 3.1 19.5 + - - +
216A LYS* 3.7 6.7 - - - +
218A THR* 1.3 75.5 + - - +
220A ARG* 1.3 63.4 + - + +
222A THR* 3.7 1.2 - - - -
223A LEU* 2.7 55.1 + - + +
249A ALA* 3.6 22.0 - - + -
252A VAL* 3.8 15.9 - - + -
253A ALA* 3.8 12.1 - - + -
256A CYS* 3.8 12.6 - - - -
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Residues in contact with ARG 220 (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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103A ARG 5.5 0.8 + - - -
104A LEU 3.2 30.1 + - - +
105A GLY* 3.5 17.5 - - - +
106A VAL* 3.7 13.9 - - + +
210A LEU* 5.0 8.6 - - - +
216A LYS* 3.0 61.1 + - - +
217A GLU* 3.8 12.0 - - - +
219A PHE* 1.3 82.7 - - + +
221A LEU* 1.3 59.8 + - - +
223A LEU* 3.0 4.3 + - - +
224A ARG* 2.8 40.2 + - - +
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Residues in contact with LEU 221 (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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38A THR* 3.7 20.9 - - + -
41A LEU* 4.8 2.0 - - + -
42A ILE* 3.8 23.8 - - + -
45A MET* 3.6 25.4 - - + -
51A PHE* 4.3 17.5 - - + -
217A GLU* 3.2 15.9 + - + +
218A THR* 4.1 2.2 - - - +
220A ARG* 1.3 77.8 - - - +
222A THR* 1.3 63.0 + - - +
224A ARG* 3.3 7.3 + - - +
225A ALA* 3.0 22.6 + - - +
264A ALA* 3.7 25.8 - - + -
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Residues in contact with THR 222 (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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218A THR 2.6 23.6 + - - -
219A PHE* 3.7 2.9 - - - -
221A LEU* 1.3 74.9 - - - +
223A LEU* 1.3 59.4 + - - +
225A ALA* 3.1 7.1 + - - +
226A VAL* 2.8 41.4 + - + +
252A VAL* 3.8 19.1 - - + -
255A THR* 6.1 1.6 - - + -
256A CYS* 5.0 1.1 - - - -
264A ALA* 3.5 8.6 - - - +
267A LEU* 3.3 38.8 - - + +
268A VAL* 3.9 19.7 - - + +
271A PHE* 5.4 1.3 - - + -
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Residues in contact with LEU 223 (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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104A LEU* 4.2 9.0 - - + -
106A VAL* 3.6 33.4 - - + -
219A PHE* 2.7 32.1 + - + +
220A ARG* 3.4 8.1 - - - +
222A THR* 1.3 72.1 - - - +
224A ARG* 1.3 63.4 + - - +
227A LYS* 2.8 49.8 + - + +
245A GLY 5.4 0.2 - - - +
248A TRP* 3.8 24.5 - - + +
249A ALA* 3.9 25.1 - - + -
252A VAL* 3.8 13.1 - - + +
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Residues in contact with ARG 224 (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 MET* 4.1 8.0 - - - +
50A VAL* 3.9 28.8 + - + +
51A PHE* 3.6 45.6 - - - +
52A GLU* 4.9 3.2 - - - +
57A LEU* 6.1 2.0 - - - +
105A GLY 3.6 23.4 + - - -
106A VAL* 3.9 25.3 + - + +
107A HIS* 4.2 18.2 + - - -
220A ARG* 2.8 28.1 + - - +
221A LEU* 3.6 13.1 - - - +
223A LEU* 1.3 71.7 - - - +
225A ALA* 1.3 63.2 + - - +
227A LYS* 4.0 3.6 - - - +
228A LEU* 3.0 24.3 + - - +
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Residues in contact with ALA 225 (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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41A LEU* 3.9 15.5 - - + -
45A MET* 3.6 20.8 - - - -
221A LEU 3.0 12.5 + - - +
222A THR 3.4 7.4 - - - +
224A ARG* 1.3 76.9 - - - +
226A VAL* 1.3 58.6 + - - +
228A LEU* 3.1 6.6 + - - +
229A TRP* 2.8 29.3 + - - +
268A VAL* 3.8 24.7 - - + -
360A LEU* 5.8 2.4 - - + +
361A LEU* 5.2 2.4 - - - +
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Residues in contact with VAL 226 (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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222A THR* 2.8 33.8 + - + +
223A LEU* 4.0 1.6 - - + +
225A ALA* 1.3 70.1 - - - +
227A LYS* 1.3 58.5 + - - +
229A TRP* 3.1 13.3 + - + +
230A ALA* 2.8 28.1 + - - +
248A TRP* 4.1 17.5 - - + -
252A VAL* 3.6 26.5 - - + -
268A VAL* 4.7 11.2 - - + -
271A PHE* 3.6 43.7 - - + -
272A PHE* 5.8 1.3 - - + -
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Residues in contact with LYS 227 (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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101A SER* 2.8 29.7 + - - +
104A LEU* 6.3 0.4 - - - +
106A VAL* 4.5 15.9 + - + +
107A HIS* 5.5 0.4 - - - +
108A THR* 6.2 1.0 - - - +
223A LEU* 2.8 49.0 + - + +
224A ARG* 4.0 3.8 - - - +
226A VAL* 1.3 77.2 - - - +
228A LEU* 1.3 61.6 + - - +
230A ALA* 3.2 7.8 + - - +
231A LYS* 2.9 43.2 + - - +
236A TYR* 3.2 31.6 - - + -
245A GLY* 4.3 7.1 + - - +
248A TRP* 4.2 11.0 - - + -
601A 3AT 3.3 18.2 + - - -
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Residues in contact with LEU 228 (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 MET* 3.8 25.4 - - + -
48A PHE* 3.7 35.9 - - + -
50A VAL* 3.8 21.1 - - + -
224A ARG 3.0 13.8 + - - +
225A ALA* 3.1 9.4 + - - +
227A LYS* 1.3 75.3 - - - +
229A TRP* 1.3 57.8 + - - +
231A LYS* 3.3 10.7 + - + +
232A ARG* 2.8 51.7 + - + +
361A LEU* 4.1 14.6 - - + -
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Residues in contact with TRP 229 (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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225A ALA 2.8 13.5 + - - +
226A VAL* 3.3 21.8 - - + +
228A LEU* 1.3 75.9 - - - +
230A ALA* 1.3 62.1 + - + +
232A ARG* 3.6 2.4 - - - +
233A ARG* 2.7 59.0 + - + +
235A ILE* 3.6 25.8 - - + -
248A TRP* 3.9 17.7 - + - -
271A PHE* 4.0 5.6 - + - -
272A PHE* 3.5 30.3 - + + -
339A GLU* 3.4 37.0 + - + -
340A PHE* 3.9 15.9 - + - -
342A GLN* 6.3 0.2 - - - +
343A GLY* 5.0 1.0 - - - -
360A LEU* 3.5 43.2 - - + +
361A LEU* 4.2 14.3 - - + +
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Residues in contact with ALA 230 (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 VAL 2.8 16.1 + - - +
227A LYS* 3.2 7.8 + - - +
229A TRP* 1.3 77.3 - - + +
231A LYS* 1.3 63.3 + - - +
233A ARG 3.2 0.7 + - - -
234A GLY 3.0 18.4 + - - -
235A ILE* 3.0 21.2 + - + -
236A TYR* 3.5 8.2 + - + -
248A TRP* 3.6 43.3 - - + +
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Residues in contact with LYS 231 (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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108A THR* 4.5 21.6 + - + +
227A LYS* 2.9 40.4 + - - +
228A LEU* 3.8 10.7 - - + +
230A ALA* 1.3 75.0 - - - +
232A ARG* 1.3 66.7 + - - +
234A GLY* 3.0 14.2 + - - -
236A TYR* 3.7 51.5 + - + +
601A 3AT 4.5 6.8 + - - -
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Residues in contact with ARG 232 (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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48A PHE* 3.3 36.8 - - + -
228A LEU* 2.8 36.8 + - + +
229A TRP* 3.8 4.7 - - - +
231A LYS* 1.3 77.8 - - - +
233A ARG* 1.3 62.1 + - + +
234A GLY 3.5 0.5 + - - -
361A LEU* 2.4 54.6 + - + +
363A PRO* 3.5 37.5 - - - +
364A PRO* 3.5 14.0 - - - +
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Residues in contact with ARG 233 (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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229A TRP* 2.7 42.2 + - + +
230A ALA* 3.9 3.8 - - - +
231A LYS 3.0 0.4 - - - -
232A ARG* 1.3 81.5 - - - +
234A GLY* 1.3 61.0 + - - +
235A ILE* 3.5 10.8 + - + +
339A GLU* 2.3 54.9 + - - +
342A GLN* 4.3 25.0 - - - +
359A LYS 5.8 1.3 + - - -
360A LEU 3.9 12.2 + - - -
361A LEU 5.2 1.1 - - - -
362A GLU* 2.7 34.0 + - - -
363A PRO 3.8 2.4 + - - -
364A PRO* 3.2 49.5 - - - +
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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
------------------------------------------------------------
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