Contacts of the strand formed by residues 242 - 260 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLU* 3.8 6.1 - - - +
234C MET* 5.0 0.3 - - - +
239C SER 5.1 0.8 + - - -
240C LYS* 3.3 48.2 - - + +
241C GLN* 1.3 103.2 - - - +
243C THR* 1.3 64.2 + - - +
283C LYS* 3.2 27.8 + - + +
284C ILE 3.2 5.6 - - - +
285C ASP* 4.5 14.5 - - - +
287C GLU* 4.8 8.0 + - - +
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Residues in contact with THR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 3.5 23.3 - - + -
94C GLU* 3.6 16.7 + - + +
96C ALA* 3.8 16.5 + - + +
234C MET* 3.8 5.5 - - - +
242C GLN* 1.3 77.5 + - - +
244C ASN* 1.3 73.8 + - - +
283C LYS* 3.6 5.2 - - - +
284C ILE* 2.7 53.9 + - + +
286C TRP* 2.9 28.1 + - - +
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Residues in contact with ASN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 3.5 1.7 - - - +
91C PRO* 3.0 25.7 - - + +
94C GLU* 3.2 16.8 + - - +
240C LYS* 5.2 6.7 - - - +
243C THR* 1.3 85.8 - - - +
245C ILE* 1.3 61.6 + - - +
281C ARG* 3.7 35.9 - - - +
282C TYR 3.5 5.1 - - - +
283C LYS* 2.7 37.9 + - - +
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Residues in contact with ILE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 4.0 9.6 - - + -
88C LEU* 4.0 21.5 - - + -
89C GLN 3.5 16.8 - - - +
90C LEU* 3.9 13.0 - - + -
91C PRO* 4.4 0.7 - - - -
98C ILE* 5.9 2.2 - - + -
230C THR* 5.9 0.4 - - + -
232C ILE* 3.5 30.5 - - + -
244C ASN* 1.3 76.4 - - - +
246C ASP* 1.3 73.1 + - - +
247C VAL* 4.8 3.1 - - + -
280C GLU 3.9 0.3 - - - +
281C ARG* 3.6 1.7 - - - +
282C TYR* 2.8 51.1 + - + +
284C ILE* 3.8 18.8 - - + -
291C MET* 4.0 8.1 - - + -
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Residues in contact with ASP 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN 3.7 0.5 - - - +
88C LEU* 3.2 4.3 - - - -
89C GLN* 2.8 48.9 + - + +
91C PRO* 4.8 4.9 - - - +
245C ILE* 1.3 73.8 - - - +
247C VAL* 1.3 61.1 + - - +
248C ILE* 3.8 13.6 - - + +
279C SER* 4.4 8.7 + - - +
280C GLU 3.4 3.8 - - - +
281C ARG* 2.6 56.8 + - - +
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Residues in contact with VAL 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 4.9 1.7 + - - -
38C VAL* 4.9 9.2 - - + -
55C ILE* 5.5 2.5 - - + -
57C THR* 4.1 15.3 - - + -
86C VAL* 4.8 1.6 - - + -
87C GLN 3.3 8.7 - - - +
88C LEU* 4.2 20.0 - - + -
245C ILE* 4.8 7.6 - - + -
246C ASP* 1.3 78.1 - - - +
248C ILE* 1.3 64.0 + - - +
249C TYR* 3.8 27.5 - - + -
278C SER 3.8 1.2 - - - +
279C SER* 3.4 1.4 - - - -
280C GLU* 2.9 32.0 + - + +
282C TYR* 3.6 33.0 - - + +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LYS 3.8 0.5 - - - +
86C VAL* 3.3 5.9 - - - -
87C GLN* 2.8 63.7 + - + +
89C GLN* 5.0 13.9 - - + +
246C ASP* 3.8 22.4 - - + +
247C VAL* 1.3 79.0 - - - +
249C TYR* 1.3 65.5 + - - +
250C GLU* 3.6 29.2 - - + +
277C ARG* 3.7 37.2 - - + +
278C SER 3.3 7.2 - - - +
279C SER* 3.7 15.5 - - - +
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Residues in contact with TYR 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C MET* 3.6 21.4 - - + +
35C HIS 4.2 6.7 - - - -
36C LYS* 3.7 41.1 - - + -
37C LYS 3.6 6.9 + - - -
38C VAL* 6.1 1.3 - - + -
57C THR* 3.5 7.9 - - + +
58C LYS 2.5 42.7 + - - -
61C ILE* 3.7 25.1 - - + -
85C LYS 3.4 3.8 - - - -
86C VAL* 4.2 16.4 - - + -
226C PRO* 4.0 12.6 - - + -
247C VAL* 3.8 23.8 - - + -
248C ILE* 1.3 80.4 - - - +
250C GLU* 1.3 61.2 + - - +
278C SER 2.8 32.4 + - - +
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Residues in contact with GLU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C MET* 3.8 5.3 - - - +
61C ILE* 3.8 6.3 - - - +
84C PHE* 3.4 4.7 - - - -
85C LYS* 2.8 58.4 + - + +
87C GLN* 4.0 18.9 + - - +
248C ILE* 3.6 10.1 - - + +
249C TYR* 1.3 79.4 - - - +
251C ARG* 1.3 62.1 + - - +
252C VAL* 4.3 3.3 - - + +
275C THR* 3.6 17.6 - - + +
276C ASP 3.2 9.4 - - - +
277C ARG* 3.6 39.9 + - + -
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLU 5.1 0.4 + - - -
32C ASN* 2.5 34.3 + - - +
33C GLY 3.7 7.7 + - - -
34C MET* 3.8 6.7 - - + +
61C ILE* 3.7 11.4 - - + +
62C ALA 2.7 33.6 + - - -
63C GLY 3.4 22.7 - - - -
64C GLN* 3.1 27.1 - - - +
81C PRO* 4.1 13.7 - - + -
83C ALA 3.4 5.6 - - - +
84C PHE* 4.6 3.4 - - + +
250C GLU* 1.3 74.3 - - - +
252C VAL* 1.3 64.7 + - - +
253C ARG* 4.0 17.1 + - + +
275C THR* 3.4 2.1 - - - +
276C ASP* 2.7 69.4 + - - +
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 3.5 4.3 - - - +
82C SER* 2.8 30.9 + - - +
83C ALA* 2.8 21.7 + - + +
85C LYS* 4.3 28.0 - - + +
250C GLU* 4.8 4.3 - - - +
251C ARG* 1.3 77.9 - - - +
253C ARG* 1.3 62.4 + - - +
272C ASP* 3.5 40.4 - - + +
274C TRP 3.4 10.3 - - - +
275C THR* 4.1 19.7 - - + +
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLY 4.9 0.7 - - - -
64C GLN* 4.9 16.9 + - - +
68C TYR* 6.2 0.6 - - - +
79C ALA* 3.7 26.1 - - - +
80C TRP 3.0 19.1 - - - +
81C PRO* 4.3 0.2 - - + -
251C ARG* 4.0 22.0 - - + +
252C VAL* 1.3 78.3 - - - +
254C ASP* 1.3 66.1 + - - +
272C ASP* 3.6 1.4 - - - -
273C LYS* 2.9 24.3 + - - +
274C TRP* 2.8 61.7 + - + +
276C ASP* 2.8 39.6 + - - +
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Residues in contact with ASP 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 3.4 6.1 - - - -
80C TRP* 2.8 52.4 + - + +
82C SER* 2.8 28.3 + - - -
184C ARG* 2.8 33.5 + - - -
253C ARG* 1.3 75.2 - - - +
255C ASP* 1.3 61.2 + - - +
269C ASN* 3.0 12.8 + - - +
270C THR 3.4 13.7 - - - +
271C LYS* 3.6 3.5 - - - -
272C ASP 2.9 17.0 + - - +
273C LYS* 4.5 0.2 - - - -
274C TRP* 3.6 3.8 - - - -
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Residues in contact with ASP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C TYR* 2.6 44.8 + - - -
78C LEU 3.6 2.1 + - - -
254C ASP* 1.3 73.1 - - - +
256C TYR* 1.3 61.4 + - - +
257C GLN* 3.0 30.2 + - - +
268C THR 3.5 2.1 - - - +
269C ASN* 3.4 4.0 - - - -
270C THR* 2.9 40.7 + - - -
273C LYS* 3.8 22.3 + - + +
274C TRP* 3.7 13.8 - - + -
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Residues in contact with TYR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLY* 3.5 0.3 - - - -
78C LEU* 2.7 43.5 + - + +
80C TRP* 3.8 18.4 - - + +
193C ASN* 2.5 36.0 + - + -
194C GLN* 3.4 13.7 - - - -
195C LEU* 3.9 20.9 - - + -
196C PHE* 3.5 35.0 - + + -
197C MET* 3.4 12.1 + - - +
210C PHE* 3.6 17.3 - + - -
254C ASP 4.0 0.4 - - - -
255C ASP* 1.3 70.9 - - - +
257C GLN* 1.3 60.0 + - - +
258C LEU* 3.7 25.6 - - + +
267C GLY* 4.3 1.6 - - - -
268C THR 3.4 13.5 - - - -
269C ASN* 3.8 14.1 + - + +
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Residues in contact with GLN 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 4.2 5.1 + - - -
69C SER* 5.1 1.9 + - - -
75C LYS* 3.5 31.0 + - - +
76C SER 3.3 8.3 - - - +
77C GLY* 4.0 7.4 - - - -
255C ASP* 3.0 39.9 + - - +
256C TYR* 1.3 74.6 - - - +
258C LEU* 1.3 62.8 + - - +
259C HIS* 5.2 0.4 + - - -
266C LYS 3.8 0.7 - - - +
267C GLY* 3.1 5.4 - - - -
268C THR* 2.8 52.6 + - - +
270C THR* 4.3 12.3 + - - -
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ASN 4.3 0.7 - - - -
75C LYS* 3.2 7.4 - - - +
76C SER 3.0 29.3 + - - -
197C MET* 3.5 35.4 - - + -
206C ALA* 4.3 5.5 - - + +
209C ASN* 3.1 45.5 - - + +
210C PHE* 3.6 30.9 - - + -
256C TYR* 3.7 15.3 - - + +
257C GLN* 1.3 72.0 - - - +
259C HIS* 1.3 61.1 + - - +
265C TRP* 4.2 13.2 - - + -
266C LYS 3.5 4.3 - - - +
267C GLY* 3.7 13.9 - - - -
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Residues in contact with HIS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASN 3.0 10.1 - - - +
75C LYS* 4.3 22.1 + - + -
257C GLN 5.2 0.8 + - - -
258C LEU* 1.3 77.0 - - - +
260C TRP* 1.3 72.7 + - - +
261C THR* 3.6 8.0 + - + +
265C TRP* 3.4 5.6 - - - -
266C LYS* 3.1 82.7 + - + +
268C THR* 4.9 12.8 - - + +
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Residues in contact with TRP 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ASN* 3.0 45.4 + - - +
201C ASN* 3.8 17.0 - - + -
202C GLY 3.5 19.3 - - - -
203C SER* 5.5 2.2 - - - -
259C HIS* 1.3 77.8 - - - +
261C THR* 1.3 63.4 + - - +
262C SER* 3.0 42.0 + - - +
263C THR* 3.6 27.6 - - - -
264C ASN* 3.7 23.6 - - - -
265C TRP* 3.4 37.9 - + + -
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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