Contacts of the helix formed by residues 216 - 234 (chain A) in PDB entry 1F5A
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A VAL* 3.4 3.5 - - - +
215A PRO* 1.3 83.6 + - + +
217A ILE* 1.3 64.6 + - - +
218A ASP* 3.2 14.0 + - - +
219A ASN* 3.0 46.4 + - + +
220A PHE* 2.9 22.0 + - - +
257A CYS* 5.3 1.1 - - - +
261A PRO 4.7 9.2 - - - +
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Residues in contact with ILE 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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211A LEU* 3.1 51.1 - - + +
214A VAL* 4.0 9.3 - - + +
215A PRO 4.2 0.4 - - - -
216A ASN* 1.3 71.1 + - - +
218A ASP* 1.3 54.2 + - - +
220A PHE* 3.1 11.0 + - + +
221A ARG* 2.7 69.7 + - - +
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASN* 3.2 9.8 + - - +
217A ILE* 1.3 82.1 - - - +
219A ASN* 1.3 65.9 + - - +
221A ARG* 3.2 25.1 + - - +
222A LEU* 3.1 22.9 + - - +
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASN* 3.0 40.4 + - + +
218A ASP* 1.3 78.4 - - - +
220A PHE* 1.3 60.7 + - - +
222A LEU* 3.6 4.2 + - - +
223A THR* 2.8 30.1 + - - -
257A CYS* 5.6 0.2 - - - -
261A PRO 5.3 1.2 + - - -
262A ASN 5.1 3.2 + - - -
263A ALA 3.4 18.4 + - - +
264A ILE* 3.7 24.1 - - - +
265A ALA* 4.3 4.5 + - - +
268A LEU* 3.9 19.0 - - + +
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.4 23.1 - - + -
210A ILE* 3.9 20.2 - - + -
211A LEU* 4.6 9.2 - - + -
214A VAL* 3.9 34.1 - - + -
216A ASN 2.9 13.2 + - - +
217A ILE* 3.2 13.7 - - + +
219A ASN* 1.3 78.3 - - - +
221A ARG* 1.3 62.9 + - + +
223A THR* 3.2 3.8 + - - -
224A LEU* 2.9 51.1 + - + +
250A ALA* 3.6 26.0 - - + -
253A VAL* 3.6 18.4 - - + -
254A ALA* 3.7 15.5 - - + -
257A CYS* 3.7 11.1 - - - -
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Residues in contact with ARG 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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104A ARG* 4.3 9.7 + - - +
105A LEU 2.8 32.6 + - - +
106A GLY* 3.7 14.2 - - - +
107A VAL* 3.7 4.1 - - + +
211A LEU* 4.7 6.3 - - - +
217A ILE* 2.7 49.3 + - - +
218A ASP* 3.4 23.2 + - - +
220A PHE* 1.3 79.3 - - + +
222A LEU* 1.3 62.2 + - - +
224A LEU* 3.2 6.7 + - - +
225A ARG* 3.0 54.3 + - - +
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Residues in contact with LEU 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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39A THR* 3.8 13.2 - - + -
42A LEU* 4.0 5.3 - - + +
43A VAL* 3.5 34.8 - - + -
46A LEU* 4.1 19.5 - - + -
52A PHE* 4.2 13.9 - - + -
218A ASP 3.1 12.4 + - - +
219A ASN* 4.1 2.0 - - - +
221A ARG* 1.3 78.7 - - - +
223A THR* 1.3 63.3 + - - +
225A ARG* 3.3 15.5 + - - +
226A ALA* 3.2 20.6 + - - +
265A ALA* 3.4 27.4 - - + -
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Residues in contact with THR 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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219A ASN 2.8 18.4 + - - -
220A PHE* 3.2 7.2 + - - -
222A LEU* 1.3 75.5 - - - +
224A LEU* 1.3 67.4 + - - +
226A ALA* 3.1 4.9 + - - +
227A ILE* 2.9 30.9 + - + +
253A VAL* 3.8 19.7 - - + -
256A THR* 5.9 1.6 - - + -
257A CYS* 5.5 0.7 - - - -
265A ALA* 3.5 6.9 - - - +
268A LEU* 3.4 26.5 - - + +
269A VAL* 3.9 33.9 - - + +
272A PHE* 5.2 2.5 - - + -
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Residues in contact with LEU 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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105A LEU* 4.2 10.3 - - + -
107A VAL* 3.4 32.8 - - + -
220A PHE* 2.9 26.0 + - + +
221A ARG* 3.5 9.2 - - - +
223A THR* 1.3 75.3 - - - +
225A ARG* 1.3 62.9 + - - +
227A ILE 3.2 0.3 + - - -
228A LYS* 2.8 52.5 + - + +
246A GLY 4.8 0.4 - - - +
249A TRP* 4.1 6.3 - - + -
250A ALA* 3.9 43.5 - - + +
253A VAL* 4.0 13.6 - - + +
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Residues in contact with ARG 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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46A LEU* 4.6 3.8 - - + -
51A VAL* 3.5 39.4 + - + +
52A PHE* 3.4 43.6 - - - +
53A GLU* 5.3 2.6 - - - +
58A LEU* 6.4 0.2 - - - +
106A GLY 2.8 21.4 + - - -
107A VAL* 3.8 17.1 - - + +
221A ARG* 3.0 48.2 + - - +
222A LEU* 3.3 15.8 - - - +
224A LEU* 1.3 78.9 - - - +
226A ALA* 1.3 62.0 + - - +
228A LYS* 3.9 4.1 - - - +
229A LEU* 3.2 22.2 + - - +
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Residues in contact with ALA 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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42A LEU* 4.4 12.3 - - + -
46A LEU* 4.3 7.1 - - + +
222A LEU 3.2 7.3 + - - +
223A THR 3.1 8.6 + - - +
225A ARG* 1.3 79.2 - - - +
227A ILE* 1.3 64.6 + - - +
229A LEU 3.2 2.1 + - - -
230A TRP* 2.9 20.7 + - - +
269A VAL* 3.8 25.6 - - + -
361A LEU* 6.0 0.2 - - - -
362A PHE* 3.4 30.8 - - + -
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Residues in contact with ILE 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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223A THR* 2.9 28.5 + - + +
224A LEU* 3.9 3.6 - - + +
226A ALA* 1.3 71.2 - - - +
228A LYS* 1.3 58.9 + - - +
230A TRP* 3.2 8.4 + - + +
231A ALA* 2.9 27.4 + - - +
249A TRP* 3.7 33.0 - - + -
253A VAL* 3.6 22.0 - - + -
269A VAL* 4.1 24.5 - - + -
272A PHE* 3.6 39.9 - - + -
273A PHE* 4.3 10.1 - - + -
361A LEU* 5.9 0.2 - - + -
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Residues in contact with LYS 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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102A SER* 3.0 13.5 + - - -
105A LEU* 6.1 0.2 - - - +
107A VAL* 3.6 31.0 + - + +
109A THR* 4.1 0.4 + - - -
224A LEU* 2.8 48.5 + - + +
225A ARG* 3.9 4.5 - - - +
227A ILE* 1.3 73.3 - - - +
229A LEU* 1.3 63.2 + - - +
231A ALA* 3.5 0.8 + - - -
232A LYS* 3.1 39.8 + - - +
237A TYR* 3.3 37.3 + - + -
246A GLY* 4.2 10.6 + - - +
249A TRP* 4.4 6.7 - - + -
1000A 3AT 2.6 24.9 + - - -
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Residues in contact with LEU 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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46A LEU* 3.7 16.2 - - + -
49A PHE* 3.7 31.9 - - + +
51A VAL* 3.8 16.4 - - + -
225A ARG 3.2 10.7 + - - +
226A ALA 3.2 8.2 + - - +
228A LYS* 1.3 78.2 - - - +
230A TRP* 1.3 55.0 + - - +
232A LYS* 3.0 13.7 + - + +
233A ARG* 2.8 55.9 + - + +
362A PHE* 3.4 30.1 - - + -
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Residues in contact with TRP 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 ALA 2.9 13.5 + - - +
227A ILE* 3.4 20.6 - - + +
229A LEU* 1.3 78.0 - - - +
231A ALA* 1.3 76.4 + - + +
233A ARG* 3.3 1.3 + - - +
234A HIS* 2.9 67.0 + + - +
236A ILE* 3.7 22.7 - - + -
249A TRP* 4.1 5.4 - + - -
272A PHE* 4.7 0.9 - + - -
273A PHE* 3.5 24.9 - + + -
340A GLU* 3.2 35.2 - - + -
341A PHE* 3.5 39.7 - + - -
344A GLY* 4.6 3.4 - - - -
347A ILE* 6.2 0.2 - - - +
361A LEU* 3.3 35.8 - - + +
362A PHE* 3.9 13.8 - - + -
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Residues in contact with ALA 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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227A ILE 2.9 19.0 + - - +
228A LYS 3.9 3.6 - - - +
230A TRP* 1.3 76.9 - - + +
232A LYS* 1.3 63.9 + - - +
234A HIS 3.2 4.9 + - - -
236A ILE* 3.0 36.4 + - + +
237A TYR* 3.9 9.0 - - + -
249A TRP* 3.5 46.2 - - + +
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Residues in contact with LYS 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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109A THR* 3.1 40.1 + - - +
228A LYS* 3.1 25.7 + - - +
229A LEU* 3.0 16.7 + - + +
231A ALA* 1.3 77.7 - - - +
233A ARG* 1.3 65.4 + - + +
234A HIS 3.0 1.2 + - - -
235A ASN* 3.1 15.8 + - - +
237A TYR* 3.6 51.8 + - + -
418A PRO* 6.0 0.2 - - - +
1000A 3AT 5.4 0.2 + - - -
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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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49A PHE* 3.4 27.6 - - - -
229A LEU* 2.8 42.7 + - + +
230A TRP 3.9 3.6 - - - +
232A LYS* 1.3 72.8 - - - +
234A HIS* 1.3 67.4 + - + +
235A ASN* 3.4 8.3 + - - +
362A PHE* 2.7 40.0 + - + +
363A GLU* 4.7 1.2 - - - +
364A ALA* 2.9 61.8 - - - +
365A PRO* 3.9 2.6 - - - +
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Residues in contact with HIS 234 (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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230A TRP* 2.9 56.6 + + + +
231A ALA 3.2 2.4 + - - +
232A LYS 3.0 0.4 - - - -
233A ARG* 1.3 83.2 - - + +
235A ASN* 1.3 76.6 + - - +
236A ILE* 3.3 17.4 + - + +
340A GLU* 3.5 32.3 + - + +
343A GLN* 6.5 1.1 - - + -
347A ILE* 5.6 8.1 - - + -
360A LYS 5.6 0.9 - - - -
361A LEU 2.9 23.9 + - - -
363A GLU 3.5 19.9 + - - -
365A PRO* 3.6 21.1 - - + +
415A HIS* 4.5 2.6 - - - -
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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