Contacts of the strand formed by residues 303 - 316 (chain C) in PDB entry 1AF6
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 THR 303 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C GLY 4.4 9.4 + - - +
293C GLN* 3.9 3.6 + - - +
294C ASP* 3.7 2.1 - - - +
295C ILE* 2.7 52.0 + - - +
301C ASN 4.7 1.1 - - - +
302C GLY* 1.3 79.2 - - - +
304C LYS* 1.3 60.8 + - - +
305C TRP* 4.1 4.2 - - - +
331C VAL* 4.0 16.6 - - + -
332C GLU 3.4 9.0 - - - +
334C GLN* 4.3 3.6 - - - +
376C TRP* 4.1 16.4 - - + -
378C TYR* 3.6 24.0 - - - +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C TYR* 3.4 38.4 + - + +
293C GLN 3.5 2.9 - - - -
294C ASP* 3.7 20.8 + - + +
303C THR* 1.3 75.0 - - - +
305C TRP* 1.3 59.8 + - - +
306C TRP* 4.8 8.8 - - + +
330C ASN* 3.8 1.9 - - - +
331C VAL* 3.5 2.0 - - - -
332C GLU* 2.8 64.3 + - + +
334C GLN* 6.5 0.4 - - - -
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Residues in contact with TRP 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 5.0 2.7 - - - +
28C ALA* 3.5 15.2 - - + +
29C GLN* 3.4 39.9 - - + -
30C SER* 3.4 28.7 - - - -
115C ILE* 5.6 0.2 - - + -
117C PHE* 4.2 7.0 - + - -
291C MET* 3.7 24.3 - - + +
292C TYR* 3.4 3.5 - - - -
293C GLN* 2.7 71.4 + - + +
303C THR* 5.3 3.6 - - - +
304C LYS* 1.3 75.1 - - - +
306C TRP* 1.3 74.7 + - - +
307C THR* 3.8 19.0 + - + -
329C ASP* 3.3 22.3 + - - -
330C ASN 3.5 8.7 - - - -
331C VAL* 3.7 23.1 - - + -
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Residues in contact with TRP 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C MET 3.4 10.3 - - - -
292C TYR* 3.3 47.5 - + + -
304C LYS* 4.8 9.7 - - + +
305C TRP* 1.3 83.2 - - - +
307C THR* 1.3 59.5 + - - +
328C TYR* 4.1 5.3 - - + +
329C ASP* 3.6 0.7 - - - -
330C ASN* 2.9 53.1 + - + +
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Residues in contact with THR 307 (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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30C SER* 5.2 2.5 - - - +
32C TYR* 3.1 27.6 - - + +
115C ILE* 5.2 5.5 - - + +
289C VAL* 5.9 2.2 - - - -
290C GLY* 3.3 2.1 - - - -
291C MET* 2.8 54.7 + - - +
305C TRP* 3.8 22.0 + - + +
306C TRP* 1.3 73.0 - - - +
308C VAL* 1.3 65.5 + - - +
328C TYR* 3.3 9.0 - - - +
329C ASP* 2.7 31.6 - - - +
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Residues in contact with VAL 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 3.0 6.3 + - - -
289C VAL 3.2 6.5 - - - +
290C GLY* 3.7 14.8 - - - -
307C THR* 1.3 81.6 - - - +
309C GLY* 1.3 60.2 - - - +
328C TYR* 2.8 51.4 + - + +
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Residues in contact with GLY 309 (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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32C TYR* 3.3 14.9 + - - -
114C MET* 3.8 6.7 - - - -
288C TYR* 3.4 2.8 - - - +
289C VAL* 2.9 31.4 + - - +
308C VAL* 1.3 76.9 - - - +
310C ILE* 1.3 66.1 + - - +
326C ILE 3.0 14.4 - - - -
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Residues in contact with ILE 310 (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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114C MET* 3.7 2.9 - - - -
286C MET* 4.2 21.3 - - + -
287C MET 3.4 7.0 - - - +
288C TYR* 4.0 14.6 - - + -
309C GLY* 1.3 80.1 - - - +
311C ARG* 1.3 61.4 + - - +
312C PRO* 3.8 16.3 - - + +
325C GLU* 3.5 3.5 - - - +
326C ILE* 2.9 55.8 + - + +
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Residues in contact with ARG 311 (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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33C ARG* 3.8 18.8 - - - +
34C LEU* 3.7 24.9 - - - +
113C HIS* 3.3 30.3 + - - -
114C MET* 3.8 22.1 - - + +
286C MET* 3.3 3.0 - - - -
287C MET* 2.7 44.4 + - + +
310C ILE* 1.3 75.2 - - - +
312C PRO* 1.3 64.5 - - - +
323C VAL* 3.8 14.4 - - + +
324C MET 3.2 10.1 - - - +
325C GLU* 2.9 43.0 + - - -
357C ILE* 3.3 15.8 + - + +
360C ARG* 3.7 11.7 - - - +
364C ARG* 4.0 10.1 - - - +
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Residues in contact with PRO 312 (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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280C MET* 6.2 1.1 - - + -
284C TRP* 4.3 21.3 - - + -
285C ASP 3.4 7.0 - - - +
286C MET* 3.9 15.4 - - + -
310C ILE* 3.7 22.7 - - + +
311C ARG* 1.3 90.5 - - - +
313C MET* 1.3 58.6 + - - +
322C THR 4.2 0.3 - - - +
323C VAL* 3.7 3.0 - - - +
324C MET* 3.1 56.4 + - + +
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Residues in contact with MET 313 (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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283C ASN 3.4 1.2 - - - +
284C TRP* 3.3 11.1 - - - -
285C ASP* 2.6 40.4 + - + +
312C PRO* 1.3 74.5 - - - +
314C TYR* 1.3 61.6 + - - +
315C LYS* 3.9 14.4 + - + +
321C SER* 3.1 37.0 - - - +
322C THR 3.5 3.6 - - - -
323C VAL* 3.9 13.9 - - + -
350C GLN* 4.1 4.9 - - - +
352C GLN* 3.6 24.5 - - - +
355C ASP 4.8 1.6 - - - -
356C SER 3.8 12.3 - - - +
357C ILE* 3.5 44.0 - - + -
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Residues in contact with TYR 314 (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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283C ASN* 3.3 41.3 + - + -
284C TRP* 3.5 42.1 - + + -
312C PRO 4.3 0.2 - - - -
313C MET* 1.3 71.9 - - - +
315C LYS* 1.3 67.2 + - - +
316C TRP* 3.5 50.8 + + - -
321C SER* 3.2 5.3 - - - -
322C THR* 2.8 45.9 + - - +
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Residues in contact with LYS 315 (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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279C SER* 4.7 1.6 + - - -
282C ASP* 3.5 24.3 + - - +
283C ASN* 2.8 42.7 + - - +
284C TRP 4.3 0.7 - - - +
285C ASP* 3.1 39.7 + - - +
313C MET* 4.3 17.9 - - + +
314C TYR* 1.3 77.1 + - - +
316C TRP* 1.3 63.7 + - - +
317C THR* 3.2 12.2 - - - +
318C PRO* 5.9 0.2 - - + -
320C MET 3.9 6.3 - - - -
321C SER* 4.1 1.6 - - - -
355C ASP* 2.6 42.6 + - + +
356C SER* 4.4 0.4 - - - +
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Residues in contact with TRP 316 (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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314C TYR* 3.7 40.3 - + - -
315C LYS* 1.3 75.1 - - - +
317C THR* 1.3 66.0 + - - +
320C MET* 3.2 20.6 + - + +
321C SER* 3.9 4.5 - - - -
322C THR* 2.8 37.8 + - - -
349C GLN* 3.9 12.7 + - - -
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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