Contacts of the strand formed by residues 242 - 260 (chain F) in PDB entry 3M4D
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 242 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLU* 3.8 1.6 - - - +
234F MET* 5.1 0.2 - - - +
240F LYS* 2.6 58.1 + - - +
241F GLN* 1.3 93.0 + - - +
243F THR* 1.3 62.3 + - - +
283F LYS* 4.3 26.2 - - + +
284F ILE 3.2 7.4 - - - +
285F ASP* 4.3 17.8 - - - +
287F GLU* 3.9 14.7 - - - +
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Residues in contact with THR 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F LEU* 3.5 21.1 - - + -
94F GLU* 3.5 18.0 + - + +
96F ALA* 3.8 17.2 + - + +
234F MET* 4.3 5.4 - - - +
240F LYS* 4.3 0.2 - - - +
242F GLN* 1.3 77.9 + - - +
244F ASN* 1.3 78.1 + - - +
283F LYS* 3.7 2.6 - - - +
284F ILE* 2.7 52.9 + - + +
286F TRP* 2.8 29.1 + - - -
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Residues in contact with ASN 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F LEU* 3.5 2.3 - - - +
91F PRO* 3.1 24.5 - - + +
94F GLU* 3.1 17.2 + - - +
240F LYS* 5.0 5.8 - - - +
243F THR* 1.3 87.2 - - - +
245F ILE* 1.3 63.3 + - - +
281F ARG* 4.1 38.5 - - - +
282F TYR 3.6 8.0 - - - +
283F LYS* 4.3 13.7 - - - +
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Residues in contact with ILE 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ILE* 4.0 9.6 - - + -
88F LEU* 4.1 21.1 - - + -
89F GLN 3.6 16.8 - - - +
90F LEU* 3.9 13.2 - - + -
91F PRO* 4.4 0.7 - - - -
98F ILE* 6.1 2.0 - - + -
232F ILE* 3.6 30.5 - - + -
244F ASN* 1.3 76.8 - - - +
246F ASP* 1.3 74.1 + - - +
247F VAL* 4.9 3.1 - - + -
280F GLU 3.9 0.5 - - - +
281F ARG* 3.6 1.1 - - - +
282F TYR* 2.8 53.7 + - + +
284F ILE* 3.9 17.7 - - + -
291F MET* 4.2 6.7 - - + -
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Residues in contact with ASP 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F GLN 3.9 0.3 - - - +
88F LEU* 3.3 4.3 - - - -
89F GLN* 2.9 44.1 + - + +
91F PRO* 4.7 2.9 - - - +
245F ILE* 1.3 73.6 - - - +
247F VAL* 1.3 61.1 + - - +
248F ILE* 3.9 14.6 - - + +
279F SER* 4.4 8.1 + - - +
280F GLU 3.4 4.3 - - - +
281F ARG* 2.7 58.2 + - - +
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Residues in contact with VAL 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LYS* 4.8 2.5 + - + -
38F VAL* 4.9 9.0 - - + -
55F ILE* 5.5 2.9 - - + -
57F THR* 4.2 13.2 - - + -
86F VAL* 5.0 0.7 - - + -
87F GLN 3.3 8.3 - - - +
88F LEU* 4.2 19.7 - - + -
245F ILE* 4.9 7.6 - - + +
246F ASP* 1.3 78.0 - - - +
248F ILE* 1.3 64.9 + - - +
249F TYR* 3.7 28.7 - - + -
278F SER 3.8 1.4 - - - +
279F SER* 3.4 1.0 - - - -
280F GLU* 2.9 32.4 + - + +
282F TYR* 3.7 33.9 - - + +
291F MET* 5.8 0.9 - - + -
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Residues in contact with ILE 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LYS 3.8 0.5 - - - +
86F VAL* 3.2 5.2 - - - -
87F GLN* 2.7 68.8 + - + +
89F GLN* 5.0 12.6 - - + +
246F ASP* 3.9 20.2 - - + +
247F VAL* 1.3 76.6 - - - +
249F TYR* 1.3 72.0 + - - +
250F GLU* 4.2 7.1 + - + +
277F ARG* 3.7 43.3 - - + +
278F SER 3.3 9.4 - - - +
279F SER* 3.5 22.9 - - - +
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Residues in contact with TYR 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F MET* 3.6 20.0 - - + +
35F HIS 4.2 4.0 - - - -
36F LYS* 3.6 43.3 - - + -
37F LYS 3.6 7.3 + - - -
38F VAL* 5.5 1.4 - - + +
57F THR* 3.4 10.5 - - + -
58F LYS 2.7 42.4 + - - -
61F ILE* 3.8 22.2 - - + -
85F LYS 3.4 3.6 - - - +
86F VAL* 3.8 18.2 - - + -
226F PRO* 4.2 9.6 - - + -
247F VAL* 3.7 23.8 - - + -
248F ILE* 1.3 82.9 - - - +
250F GLU* 1.3 63.2 + - - +
278F SER* 2.8 33.2 + - - +
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Residues in contact with GLU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F MET* 3.9 4.9 - - - +
61F ILE* 3.8 5.8 - - - +
83F ALA 4.7 0.2 - - - -
84F PHE* 3.5 3.6 - - - -
85F LYS* 2.8 73.6 + - + +
87F GLN* 4.6 9.2 + - - +
248F ILE* 4.7 7.0 - - + +
249F TYR* 1.3 75.6 - - - +
251F ARG* 1.3 66.0 + - - +
252F VAL* 4.0 4.8 - - + +
275F THR* 3.6 26.4 - - + +
276F ASP 3.2 14.6 - - - +
277F ARG* 3.5 27.4 + - - +
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Residues in contact with ARG 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F GLU 5.1 0.2 + - - -
32F ASN* 2.5 35.1 + - - +
33F GLY 3.7 4.8 + - - -
34F MET* 4.0 6.5 - - + +
61F ILE* 3.6 15.6 - - + +
62F ALA 2.7 31.4 + - - -
63F GLY 3.5 22.0 - - - -
64F GLN* 3.1 26.7 - - - +
81F PRO* 4.2 12.6 - - + -
83F ALA 3.5 5.8 - - - +
84F PHE* 4.6 3.4 - - + +
250F GLU* 1.3 76.0 - - - +
252F VAL* 1.3 64.7 + - - +
253F ARG* 4.0 17.6 + - + +
275F THR* 3.4 2.4 - - - +
276F ASP* 2.8 70.6 + - - +
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Residues in contact with VAL 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PRO* 3.5 4.3 - - - +
82F SER* 2.9 29.6 + - - +
83F ALA* 2.9 22.9 + - + +
85F LYS* 4.2 20.4 - - + +
250F GLU* 4.0 20.0 - - + +
251F ARG* 1.3 76.8 - - - +
253F ARG* 1.3 62.8 + - - +
272F ASP* 3.5 42.0 - - + +
274F TRP 3.5 7.6 - - - +
275F THR* 4.1 12.3 - - + +
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Residues in contact with ARG 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLY 4.9 0.9 - - - -
64F GLN* 4.8 18.9 + - - +
66F ARG* 6.3 0.6 - - - +
79F ALA* 4.0 17.3 - - - +
80F TRP 3.1 17.5 - - - +
81F PRO 4.2 0.2 - - - -
251F ARG* 4.1 19.5 - - + +
252F VAL* 1.3 77.2 - - - +
254F ASP* 1.3 65.1 + - - +
272F ASP* 3.6 0.9 - - - -
273F LYS* 2.9 24.8 + - - +
274F TRP* 2.7 71.5 + - + +
276F ASP* 2.8 40.8 + - - +
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Residues in contact with ASP 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ALA* 3.4 6.8 - - - -
80F TRP* 2.8 50.9 + - + +
82F SER* 2.6 27.9 + - - -
184F ARG* 2.8 38.6 + - - -
253F ARG* 1.3 75.1 - - - +
255F ASP* 1.3 60.9 + - - +
256F TYR 4.0 0.7 - - - -
269F ASN* 3.1 11.3 + - - +
270F THR 3.4 12.8 - - - +
271F LYS* 3.6 1.7 - - - -
272F ASP 2.9 16.9 + - - +
274F TRP* 3.6 3.4 - - - -
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Residues in contact with ASP 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F TYR* 2.5 40.9 + - - -
78F LEU 3.7 1.8 - - - -
254F ASP* 1.3 71.6 - - - +
256F TYR* 1.3 61.8 + - - +
257F GLN* 3.3 27.5 + - - +
268F THR 3.5 2.1 - - - +
269F ASN* 3.3 4.4 - - - -
270F THR* 2.8 51.0 + - - -
273F LYS* 3.9 23.7 - - + +
274F TRP* 3.7 10.0 - - + -
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Residues in contact with TYR 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F GLY* 3.6 0.2 - - - -
78F LEU* 2.7 48.0 + - + +
80F TRP* 3.9 16.4 - - + -
193F ASN* 2.7 42.7 + - + -
194F GLN 3.5 0.3 - - - -
195F LEU* 4.1 3.4 - - + -
196F PHE* 3.4 47.2 + + + -
197F MET* 3.3 23.4 + - - +
210F PHE* 3.5 33.1 - + - -
254F ASP 4.0 0.6 - - - -
255F ASP* 1.3 71.5 + - - +
257F GLN* 1.3 60.1 + - - +
258F LEU* 3.9 16.4 - - + +
267F GLY* 4.4 1.6 - - - -
268F THR 3.3 14.1 - - - -
269F ASN* 3.8 14.1 + - + +
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Residues in contact with GLN 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F TYR* 4.1 4.2 + - - -
69F SER* 5.9 0.4 - - - -
76F SER 3.5 6.4 - - - +
77F GLY* 4.1 10.3 - - - -
255F ASP* 3.3 37.0 + - - +
256F TYR* 1.3 75.5 - - - +
258F LEU* 1.3 64.0 + - - +
259F HIS* 5.2 0.8 + - - -
266F LYS 3.8 0.7 - - - +
267F GLY* 3.2 4.9 - - - -
268F THR* 2.6 55.3 + - - +
270F THR* 4.6 10.5 + - - -
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Residues in contact with LEU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ASN 4.2 0.7 - - - -
75F LYS* 3.4 3.8 - - - +
76F SER 3.1 27.7 + - - +
197F MET* 3.8 35.2 - - + -
206F ALA* 4.2 5.4 - - + +
209F ASN* 3.3 44.9 - - + +
210F PHE* 3.4 35.9 - - + -
256F TYR* 3.9 17.9 - - + +
257F GLN* 1.3 74.7 - - - +
259F HIS* 1.3 63.5 + - - +
265F TRP* 4.4 11.4 - - + -
266F LYS 3.4 3.4 - - - +
267F GLY* 3.9 6.7 - - - -
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Residues in contact with HIS 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ASN 2.9 11.0 - - - +
75F LYS* 3.8 25.6 - - + -
257F GLN 5.2 1.4 + - - -
258F LEU* 1.3 77.1 - - - +
260F TRP* 1.3 72.2 + - - +
261F THR* 3.5 9.2 + - + +
265F TRP* 3.6 5.5 - - - -
266F LYS* 3.0 84.2 + - + +
268F THR* 4.9 10.9 + - - -
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Residues in contact with TRP 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ASN* 2.9 45.8 + - - +
201F ASN* 3.8 18.6 - - + -
202F GLY 4.0 4.9 - - - -
203F SER* 6.0 1.1 - - - -
259F HIS* 1.3 76.4 - - - +
261F THR* 1.3 61.1 + - - +
262F SER* 3.3 42.5 + - - +
263F THR* 3.6 19.1 - - - -
264F ASN* 3.4 29.8 - - - -
265F TRP* 3.6 44.7 - + + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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