Contacts of the strand formed by residues 226 - 238 (chain A) in PDB entry 4LL1
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 GLN 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.5 4.9 - - - -
223A ALA 3.0 35.1 + - - +
224A ASN* 3.1 6.1 + - + -
225A GLY* 1.3 97.4 - - - +
227A THR* 1.3 70.9 + - - +
228A LYS* 4.3 11.2 - - + -
71C ARG 5.5 4.5 - - - +
72C TYR* 3.0 43.8 - - + +
73C GLU 6.2 0.2 - - - +
103C PHE* 4.7 4.6 - - - +
104C GLU* 4.8 13.4 + - - +
225C GLY* 3.6 9.9 + - - -
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Residues in contact with THR 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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220A THR* 3.2 35.4 - - + -
221A TYR 3.4 4.7 - - - +
222A LEU* 3.8 9.0 - - - +
226A GLN* 1.3 74.9 + - - +
228A LYS* 1.3 66.0 + - - +
270A LEU* 3.6 18.3 - - + +
271A ARG* 5.6 0.4 - - - +
225C GLY 4.6 2.1 + - - -
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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
----------------------------------------------------------
220A THR* 3.3 4.9 - - - -
221A TYR* 3.0 64.6 + - + +
223A ALA* 4.7 15.9 - - - +
224A ASN* 6.0 3.1 - - - -
226A GLN* 3.8 15.5 + - + -
227A THR* 1.3 78.3 - - - +
229A VAL* 1.3 63.2 + - - +
72C TYR* 5.4 5.2 - - + +
73C GLU* 3.0 43.3 + - - +
74C ASP* 3.2 23.9 - - - +
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Residues in contact with VAL 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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218A ARG* 3.9 30.1 - - + -
219A HIS 2.8 15.9 - - - +
220A THR* 4.3 10.5 - - - +
221A TYR* 4.0 3.6 - - - -
228A LYS* 1.3 75.8 - - - +
230A LEU* 1.3 64.3 + - - +
231A THR* 4.6 5.6 - - - +
273A GLU* 6.4 0.4 - - - -
74C ASP* 5.4 3.8 + - - +
85C GLU* 3.9 12.8 - - - +
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Residues in contact with LEU 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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217A ALA 3.4 2.6 - - - +
218A ARG* 3.3 1.7 - - - -
219A HIS* 2.7 53.3 + - + +
221A TYR* 3.7 20.2 - - + +
229A VAL* 1.3 73.7 - - - +
231A THR* 1.3 65.2 + - - +
232A GLN* 5.1 4.0 - - + +
85C GLU* 3.6 29.6 - - + +
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Residues in contact with THR 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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216A VAL* 4.4 10.1 - - + -
217A ALA 3.5 2.7 - - - +
218A ARG* 4.0 31.1 - - + +
229A VAL* 4.6 5.2 - - - +
230A LEU* 1.3 72.9 - - - +
232A GLN* 1.3 61.4 + - - +
77C LEU* 4.1 8.7 - - + +
82C PRO 4.3 8.7 - - - +
83C THR 4.0 11.5 - - - +
84C GLY* 3.8 21.5 - - - -
85C GLU* 3.2 43.1 + - - +
86C ASN 5.0 1.0 + - - -
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Residues in contact with GLN 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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216A VAL* 3.1 6.7 - - - +
217A ALA* 2.7 44.5 + - + +
219A HIS* 3.1 28.4 - - + +
230A LEU* 3.8 5.3 + - + -
231A THR* 1.3 75.2 - - - +
233A LYS* 1.3 65.0 + - - +
234A LEU* 3.5 24.2 + - + +
260A ILE* 3.3 15.2 - - - +
83C THR 4.2 3.6 - - - -
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Residues in contact with LYS 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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214A ALA* 4.1 16.6 - - + -
215A ILE 3.7 3.1 - - - -
216A VAL* 4.3 2.5 - - + -
232A GLN* 1.3 77.7 + - - +
234A LEU* 1.3 73.4 + - - +
236A SER* 3.6 32.0 + - - -
279A TYR* 5.1 5.4 + - - -
83C THR* 3.7 41.1 + - - +
86C ASN* 6.4 2.0 - - + -
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Residues in contact with LEU 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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215A ILE* 2.7 33.2 + - + +
217A ALA* 4.2 9.0 - - + -
232A GLN* 3.5 37.9 - - + +
233A LYS* 1.3 84.7 - - - +
235A SER* 1.3 71.3 + - - +
236A SER* 3.5 3.6 + - - -
257A VAL* 6.3 1.1 - - + -
258A GLN* 3.9 36.3 - - + +
260A ILE* 3.9 22.7 - - + -
274A TYR* 4.0 20.2 - - + -
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Residues in contact with SER 235 (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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214A ALA* 3.3 1.7 - - - +
215A ILE* 2.9 40.9 + - - +
234A LEU* 1.3 80.5 - - - +
236A SER* 1.3 59.8 + - - +
255A LEU* 3.6 12.7 - - - +
256A ARG* 2.4 35.3 + - - -
258A GLN* 3.6 19.9 + - - +
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Residues in contact with SER 236 (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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213A ALA 3.2 12.1 - - - -
214A ALA* 4.0 1.6 - - - -
233A LYS* 3.6 33.3 + - - -
234A LEU 3.5 2.0 + - - -
235A SER* 1.3 77.4 - - - +
237A VAL* 1.3 71.2 + - - +
255A LEU* 3.7 5.9 - - - +
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Residues in contact with VAL 237 (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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197A ILE* 5.1 0.9 - - + -
212A LYS* 3.3 7.5 - - - +
213A ALA* 2.8 52.0 + - + +
236A SER* 1.3 80.9 - - - +
238A ARG* 1.3 63.2 + - - +
250A TRP* 4.1 13.5 - - + -
253A LYS* 4.3 26.2 - - + +
254A SER 4.0 13.2 - - - +
255A LEU* 4.0 19.3 - - + -
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Residues in contact with ARG 238 (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 VAL* 3.9 36.4 - - + +
211A PRO 3.9 2.0 - - - -
212A LYS* 4.0 26.3 - - + +
237A VAL* 1.3 76.1 - - - +
239A GLY* 1.3 69.6 + - - +
241A HIS* 5.8 2.2 - - - +
250A TRP* 4.7 3.1 - - - -
253A LYS* 3.8 14.7 + - - -
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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