Contacts of the strand formed by residues 219 - 233 (chain A) in PDB entry 3CMT
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 ALA 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ILE* 3.3 14.6 - - - +
63A GLU* 4.3 10.8 - - + +
215A LEU* 2.9 21.1 + - + +
216A LYS 4.2 0.9 - - - +
217A PHE 3.4 0.9 - - - +
218A TYR* 1.3 75.9 - - - +
220A SER* 1.3 60.9 + - - +
221A VAL 3.8 8.7 - - - +
222A ARG* 3.7 29.4 - - + -
248A LYS* 3.0 29.0 + - - -
250A LYS* 4.1 2.3 - - - +
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Residues in contact with SER 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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57A PRO* 4.4 8.7 - - - -
60A ARG* 3.0 52.1 + - - +
61A ILE 2.8 11.9 + - - -
218A TYR 4.0 5.7 + - - -
219A ALA* 1.3 74.3 - - - +
221A VAL* 1.3 64.5 + - - +
248A LYS* 4.5 2.4 - - - +
249A ASN* 3.5 2.1 + - - -
250A LYS* 2.8 44.8 + - - +
251A ILE* 4.5 1.3 + - - -
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Residues in contact with VAL 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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51A LEU* 3.6 20.9 - - + -
56A LEU* 4.1 8.3 - - + -
57A PRO* 4.1 24.9 - - + -
61A ILE 3.8 1.8 + - - -
62A VAL* 3.4 16.5 - - + +
63A GLU 3.0 23.7 + - - -
219A ALA* 3.3 1.6 - - - +
220A SER* 1.3 85.6 - - - +
222A ARG* 1.3 68.1 + - - +
223A LEU* 3.5 27.1 - - + -
246A VAL* 4.6 1.1 - - + -
248A LYS 3.2 8.7 - - - +
249A ASN* 3.7 16.8 - - - +
251A ILE* 4.8 4.0 - - + -
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Residues in contact with ARG 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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63A GLU* 2.5 50.1 + - + +
65A TYR* 3.7 29.8 + - + -
209A THR* 4.4 8.5 + - - +
216A LYS* 4.1 44.9 + - - +
219A ALA* 3.7 19.3 - - + -
221A VAL* 1.3 79.5 - - - +
223A LEU* 1.3 67.7 + - - +
246A VAL* 3.7 0.5 - - - -
247A VAL* 2.8 41.5 + - + +
248A LYS* 2.9 34.5 + - + +
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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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47A LEU* 4.5 17.5 - - + -
51A LEU* 4.3 4.0 - - + -
56A LEU* 4.2 22.7 - - + -
62A VAL* 4.6 1.8 - - + -
63A GLU 2.7 12.2 + - - +
64A ILE* 3.4 31.9 - - + +
65A TYR* 2.9 34.7 + - - +
75A LEU* 4.9 4.3 - - + -
221A VAL* 3.5 19.7 - - + -
222A ARG* 1.3 79.7 - - - +
224A ASP* 1.3 58.9 + - - +
225A ILE 3.8 0.4 + - - -
244A VAL* 3.7 21.1 - - + -
245A LYS 3.4 1.6 - - - +
246A VAL* 4.0 25.8 - - + -
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Residues in contact with ASP 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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65A TYR* 3.5 30.3 + - + +
66A GLY* 4.8 0.2 - - - -
207A GLU* 5.0 0.3 - - - +
222A ARG 4.2 0.2 + - - -
223A LEU* 1.3 70.7 - - - +
225A ILE* 1.3 62.8 + - - +
226A ARG* 2.7 40.8 + - - -
243A ARG 3.6 1.6 - - - +
244A VAL* 3.3 3.1 - - - -
245A LYS* 2.8 47.7 + - + +
247A VAL* 3.5 24.5 - - + +
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Residues in contact with ILE 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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64A ILE* 3.8 13.9 - - + -
65A TYR 3.0 17.9 + - - +
66A GLY* 3.4 2.6 - - - -
67A PRO* 3.3 14.6 - - - +
70A SER* 3.6 26.3 - - - +
71A GLY* 3.8 18.8 - - - +
72A LYS* 3.6 27.1 - - + -
75A LEU* 4.0 15.9 - - + -
223A LEU 3.8 0.8 - - - -
224A ASP* 1.3 73.8 - - - +
226A ARG* 1.3 73.1 + - - +
242A THR* 3.7 21.5 - - + -
243A ARG 3.5 2.5 - - - -
244A VAL* 3.8 18.2 - - + +
260A PHE* 4.7 0.7 - - + -
262A ILE* 4.8 2.2 - - + -
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Residues in contact with ARG 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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65A TYR* 4.6 1.6 - - - -
67A PRO* 3.4 25.8 - - + +
70A SER* 4.2 9.0 - - - -
195A ILE* 3.2 19.5 - - - +
207A GLU* 2.6 40.1 + - - -
224A ASP* 2.7 34.3 + - - +
225A ILE* 1.3 80.2 - - - +
227A ARG* 1.3 65.6 + - - +
228A ILE* 3.6 9.3 + - + +
242A THR* 3.6 3.2 - - - +
243A ARG* 2.9 41.9 + - + +
245A LYS* 5.9 5.4 - - - +
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Residues in contact with ARG 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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67A PRO* 5.5 1.4 - - - +
68A GLU 6.1 0.4 - - - +
69A SER 4.6 7.6 - - - +
70A SER* 4.2 21.3 + - - +
226A ARG* 1.3 73.9 - - - +
228A ILE* 1.3 63.1 + - - +
229A GLY* 3.6 26.8 + - - +
230A ALA* 3.5 27.9 - - - +
237A VAL* 4.0 0.2 - - - +
239A GLY 4.0 1.4 + - - -
240A SER* 3.0 23.9 + - - +
241A GLU 3.6 5.8 - - - +
242A THR* 4.7 3.4 - - - +
264A TYR* 3.6 7.1 + - - -
502A ADP 5.3 0.4 + - - -
1255A PHE* 3.1 43.9 - - - -
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Residues in contact with ILE 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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226A ARG* 3.9 8.7 - - + +
227A ARG* 1.3 79.5 - - - +
229A GLY* 1.3 58.6 + - - +
241A GLU* 2.8 37.5 + - + +
242A THR 4.2 4.7 - - - +
243A ARG* 3.6 55.0 - - + +
259A GLU* 4.0 21.3 - - + +
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Residues in contact with GLY 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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227A ARG* 3.6 23.0 - - - +
228A ILE* 1.3 81.4 - - - +
230A ALA* 1.3 56.9 + - - -
240A SER* 3.7 0.3 - - - -
241A GLU* 2.8 36.6 + - - +
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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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227A ARG* 3.5 24.4 - - - +
229A GLY* 1.3 73.0 - - - -
231A VAL* 1.3 62.1 + - - +
232A LYS* 3.6 23.1 + - + +
237A VAL* 4.0 17.9 - - + -
239A GLY 3.7 0.9 - - - -
241A GLU* 4.5 4.6 - - - +
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Residues in contact with VAL 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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230A ALA* 1.3 69.2 - - - +
232A LYS* 1.3 65.0 + - - +
237A VAL* 3.7 2.3 - - - -
238A VAL* 2.9 44.2 + - + +
239A GLY* 2.8 29.8 + - - +
240A SER 4.0 1.6 - - - +
241A GLU* 3.4 31.6 - - - +
261A GLN* 3.5 30.7 - - + +
263A LEU* 4.0 12.6 - - + -
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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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230A ALA* 3.6 19.2 + - + +
231A VAL* 1.3 80.3 - - - +
233A GLU* 1.3 62.8 + - - +
234A GLY* 3.5 22.0 + - - +
235A GLU 4.8 3.4 - - - +
236A ASN 3.2 10.3 - - - +
237A VAL* 4.2 17.7 - - + -
238A VAL* 4.7 0.9 - - - -
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Residues in contact with GLU 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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231A VAL 4.2 0.2 + - - -
232A LYS* 1.3 71.8 - - - +
234A GLY* 1.3 52.7 + - - +
235A GLU* 2.7 16.8 + - - +
236A ASN* 2.7 36.8 + - + +
238A VAL* 3.9 26.0 - - + -
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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