Contacts of the strand formed by residues 396 - 416 (chain A) in PDB entry 3C0M
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 VAL 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.8 14.8 - - + +
93A ILE* 3.9 22.2 - - + -
101A VAL* 6.3 0.4 - - + -
105A LEU* 4.2 26.9 - - + -
112A PHE* 6.2 0.2 - - + -
311A ASP* 3.9 1.2 - - - +
312A VAL* 2.9 57.6 + - + +
314A TYR* 4.6 16.6 - - + +
345A ILE* 6.5 0.2 - - + -
394A ARG* 3.4 11.8 + - + +
395A PRO* 1.3 75.9 - - - +
397A ARG* 1.3 68.9 + - - +
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Residues in contact with ARG 397 (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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90A ALA* 3.3 27.8 - - + +
91A LEU 3.1 8.3 + - - -
92A ASP* 3.2 35.3 + - - +
93A ILE* 2.6 35.5 + - - +
180A ASP* 4.8 7.5 + - - -
183A SER* 4.8 7.7 - - - -
309A LYS* 4.2 32.1 - - + +
310A ALA 3.4 7.6 - - - +
311A ASP* 3.4 25.4 - - - +
312A VAL* 4.0 2.9 - - - -
395A PRO* 4.0 3.5 + - + -
396A VAL* 1.3 82.9 - - - +
398A ALA* 1.3 57.6 + - - +
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 3.6 9.2 - - + +
95A ASP* 5.6 1.6 - - - -
101A VAL* 4.7 12.8 - - + -
177A TYR* 5.6 0.4 - - + -
235A LEU* 3.8 29.6 - - + -
309A LYS* 3.5 5.0 - - - -
310A ALA* 2.7 38.7 + - + +
312A VAL* 3.8 12.4 - - + +
397A ARG* 1.3 75.3 - - - +
399A GLY* 1.3 59.4 + - - +
400A ILE* 3.4 4.3 - - + +
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Residues in contact with GLY 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE 3.4 12.3 + - - -
95A ASP* 2.9 34.7 - - - +
235A LEU* 5.4 0.7 - - - +
307A GLU* 4.7 5.2 - - - -
308A PHE 3.7 6.7 - - - -
309A LYS* 3.9 18.2 - - - +
398A ALA* 1.3 72.5 - - - +
400A ILE* 1.3 66.3 + - - +
401A THR* 4.7 2.7 - - - -
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Residues in contact with ILE 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP* 3.5 4.5 - - - +
179A LEU* 4.6 12.3 - - + -
231A ASN* 6.1 0.2 - - - -
235A LEU* 4.7 9.2 - - + -
236A SER* 4.9 11.0 - - - +
239A VAL* 4.3 17.5 - - + -
265A TRP* 3.7 36.1 - - + +
306A TYR* 3.8 4.5 - - + -
307A GLU* 3.4 2.6 - - - -
308A PHE* 2.8 35.6 + - + +
309A LYS 4.5 0.4 - - - -
310A ALA* 3.2 37.7 - - + +
398A ALA* 3.4 12.3 - - + +
399A GLY* 1.3 80.6 - - - +
401A THR* 1.3 66.9 + - - +
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Residues in contact with THR 401 (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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95A ASP* 3.1 21.5 + - + +
231A ASN* 3.7 2.8 - - - +
232A THR* 3.2 30.8 + - - +
233A TYR* 4.7 2.4 + - - -
236A SER* 5.5 0.5 + - - -
306A TYR* 3.7 18.9 + - - +
307A GLU* 3.2 43.1 - - + +
399A GLY 4.7 2.2 - - - -
400A ILE* 1.3 79.4 - - - +
402A GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 402 (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 THR* 3.3 18.2 - - - -
232A THR* 3.9 13.0 + - - -
305A PRO* 3.6 7.3 - - - +
306A TYR* 3.3 31.9 + - - +
401A THR* 1.3 78.2 - - - +
403A ASP* 1.3 62.3 + - - +
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Residues in contact with ASP 403 (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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228A SER 4.6 0.2 - - - -
229A LYS* 2.9 9.9 - - - +
230A THR* 2.6 49.0 + - + +
304A TYR 4.1 2.6 - - - +
305A PRO* 3.7 24.9 - - - +
306A TYR* 3.6 2.4 - - - -
402A GLY* 1.3 76.3 - - - +
404A PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 404 (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 TRP* 3.5 26.5 - + + -
228A SER 3.5 11.2 - - - -
229A LYS* 4.2 2.7 - - + -
247A TRP* 3.5 39.7 - + + -
255A LEU* 3.7 21.3 - - + -
257A ILE* 3.3 26.7 - - + -
302A ILE* 4.4 4.7 - - + -
303A SER* 3.2 3.5 - - - -
304A TYR* 3.0 71.1 + + + +
306A TYR* 4.0 9.4 - - + -
403A ASP* 1.3 76.3 - - - +
405A SER* 1.3 62.8 + - - +
406A ALA* 3.7 15.3 - - + -
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Residues in contact with SER 405 (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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191A GLN* 5.4 1.1 - - - -
226A ASN 4.2 0.2 - - - +
227A TRP* 3.2 3.3 - - - +
228A SER* 2.8 46.1 + - - +
302A ILE 3.1 11.0 - - - -
303A SER* 3.7 13.2 - - - -
404A PHE* 1.3 80.8 - - - +
406A ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 406 (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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225A THR* 4.5 2.5 - - + -
226A ASN 3.4 6.5 - - - +
227A TRP* 3.9 9.6 - - + -
255A LEU* 3.7 38.8 - - + -
301A ASP* 3.1 7.2 - - - +
302A ILE* 3.0 32.2 + - + +
404A PHE* 3.7 11.2 - - + -
405A SER* 1.3 76.5 - - - +
407A GLU* 1.3 60.9 + - - +
408A SER 4.3 0.2 - - - -
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Residues in contact with GLU 407 (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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224A ALA 4.1 0.3 - - - +
225A THR* 3.1 4.6 - - - +
226A ASN* 2.8 49.5 + - + +
299A LYS* 5.2 15.5 + - + +
300A ALA 3.8 6.3 - - - +
301A ASP* 3.9 18.8 - - + +
406A ALA* 1.3 75.4 - - - +
408A SER* 1.3 65.0 + - - +
409A GLN* 6.1 2.0 - - + -
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ALA 3.5 6.3 - - - -
225A THR* 3.3 27.6 - - - -
253A THR* 4.6 2.1 + - - -
254A GLU 2.9 22.3 + - - -
255A LEU* 3.5 9.7 - - - +
299A LYS* 3.4 4.3 - - - +
300A ALA 3.1 34.6 + - - +
407A GLU* 1.3 78.0 - - - +
409A GLN* 1.3 68.2 + - - +
410A PHE* 4.3 8.2 - - - -
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Residues in contact with GLN 409 (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 VAL* 5.8 1.2 - - - +
223A THR* 2.8 38.5 - - - +
224A ALA 3.4 7.4 + - - +
225A THR* 5.3 0.3 + - - -
298A TYR 3.1 11.9 - - - +
299A LYS* 4.2 18.4 - - + +
407A GLU* 6.1 2.6 - - + -
408A SER* 1.3 82.7 - - - +
410A PHE* 1.3 66.1 + - - +
455A LEU 2.6 30.3 + - - +
456A GLY* 2.9 22.4 - - - +
457A PHE* 3.2 12.1 - - + -
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Residues in contact with PHE 410 (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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194A ARG* 4.8 17.5 - - - -
223A THR* 4.5 6.5 - - + -
252A GLU 5.8 0.7 - - - -
253A THR* 5.0 1.8 - - - -
254A GLU* 3.5 59.7 - - + +
277A LEU* 6.0 1.3 - - - -
297A LEU* 3.7 0.3 - - - -
298A TYR* 2.7 75.5 + + + +
300A ALA* 4.6 11.9 - - + -
408A SER* 4.3 12.1 - - - -
409A GLN* 1.3 80.1 - - - +
411A ALA* 1.3 71.7 + - - +
412A GLY* 5.5 0.2 - - - -
457A PHE* 4.2 10.1 - - - -
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Residues in contact with ALA 411 (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 LEU* 4.7 6.1 - - + -
254A GLU* 4.9 1.7 - - - +
277A LEU* 4.0 25.8 - - + +
279A GLN* 5.2 4.8 + - - +
295A ILE* 4.5 7.6 - - + -
296A GLU 3.4 4.9 - - - +
297A LEU* 3.6 20.4 - - + -
298A TYR* 4.3 0.2 - - - -
410A PHE* 1.3 90.0 - - - +
412A GLY* 1.3 71.3 + - - +
413A ASN* 5.2 0.7 + - - -
457A PHE* 4.6 0.8 - - - -
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Residues in contact with GLY 412 (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 LEU* 5.9 0.3 - - - +
279A GLN* 2.8 14.9 + - - +
295A ILE* 4.9 2.5 - - - +
296A GLU* 2.7 23.0 + - - +
298A TYR* 4.0 14.8 - - - -
410A PHE* 5.3 0.7 - - - -
411A ALA* 1.3 84.6 - - - +
413A ASN* 1.3 70.7 + - - -
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Residues in contact with ASN 413 (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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279A GLN* 2.8 20.0 + - + +
294A LYS 3.5 7.6 - - - +
295A ILE* 4.0 8.8 - - - -
296A GLU 4.5 1.2 + - - -
411A ALA 5.2 0.4 + - - -
412A GLY* 1.3 81.6 - - - -
414A ILE* 1.3 70.3 + - - +
415A GLU* 3.5 21.2 + - + +
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Residues in contact with ILE 414 (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 VAL* 3.8 31.4 - - + +
219A LEU* 4.2 17.3 - - + +
279A GLN* 3.5 37.6 + - + +
281A VAL* 3.4 33.7 - - + +
293A VAL* 4.9 10.3 - - + -
294A LYS 3.6 7.4 - - - +
295A ILE* 4.1 21.3 - - + -
413A ASN* 1.3 77.4 - - - +
415A GLU* 1.3 66.7 + - - +
416A ILE* 4.3 6.9 + - + -
462A LEU* 4.7 4.3 - - + -
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Residues in contact with GLU 415 (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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293A VAL* 3.2 5.4 - - - +
294A LYS* 2.8 51.3 + - + +
296A GLU* 4.5 6.8 - - - +
413A ASN* 3.6 21.8 + - + +
414A ILE* 1.3 78.4 - - - +
416A ILE* 1.3 62.8 + - - +
114B LYS* 2.8 35.4 + - - +
118B TYR* 2.7 33.6 + - - +
135B TYR* 3.5 16.3 - - + +
138B GLU* 4.1 6.1 - - - +
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Residues in contact with ILE 416 (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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281A VAL* 4.3 21.8 - - + -
283A PRO* 3.5 32.1 - - + -
284A THR 5.3 0.4 - - - +
291A ILE* 3.8 24.2 - - + -
292A PRO 3.4 3.6 - - - -
293A VAL* 4.6 10.8 - - + -
414A ILE* 4.9 6.1 - - + +
415A GLU* 1.3 78.8 - - - +
417A GLY* 1.3 62.7 + - - +
118B TYR* 4.8 5.8 + - + -
135B TYR* 3.8 8.1 - - - -
136B VAL* 4.7 13.2 - - - +
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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
------------------------------------------------------------
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