Contacts of the strand formed by residues 303 - 316 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY 4.3 10.1 + - - +
293A GLN* 3.9 3.3 + - - +
294A ASP* 3.7 2.3 - - - +
295A ILE* 2.7 55.5 + - - +
301A ASN 4.8 0.4 - - - +
302A GLY* 1.3 79.7 - - - +
304A LYS* 1.3 59.9 + - - +
305A TRP* 4.1 4.4 - - - +
331A VAL* 4.0 15.3 - - + -
332A GLU 3.4 8.5 - - - +
334A GLN* 4.3 3.8 - - - +
376A TRP* 4.1 16.2 - - + -
378A TYR* 3.6 24.2 - - - +
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Residues in contact with LYS 304 (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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292A TYR* 3.4 41.9 + - + +
293A GLN 3.5 3.1 - - - +
294A ASP* 3.9 17.3 + - - +
303A THR* 1.3 75.0 - - - +
305A TRP* 1.3 59.9 - - - +
306A TRP* 4.8 10.3 - - + +
330A ASN* 3.8 1.7 - - - +
331A VAL* 3.5 1.6 - - - -
332A GLU* 2.8 63.1 + - + +
334A GLN* 6.5 0.4 - - - -
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Residues in contact with TRP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 4.9 3.1 - - - +
28A ALA* 3.6 14.8 - - + +
29A GLN* 3.4 38.6 - - + -
30A SER* 3.4 28.5 - - - -
115A ILE* 5.5 0.2 - - + -
117A PHE* 4.2 6.1 - + - -
291A MET* 3.6 25.8 - - + +
292A TYR* 3.4 3.5 - - - -
293A GLN* 2.7 73.1 + - + +
303A THR* 5.2 4.3 - - - +
304A LYS* 1.3 75.3 - - - +
306A TRP* 1.3 73.4 + - - +
307A THR* 3.7 19.6 + - - -
329A ASP* 3.2 22.8 + - - -
330A ASN 3.4 9.2 - - - -
331A VAL* 3.7 23.1 - - + +
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Residues in contact with TRP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A MET 3.4 9.0 - - - -
292A TYR* 3.3 49.5 - + + -
304A LYS* 4.8 10.5 - - + +
305A TRP* 1.3 84.2 - - - +
307A THR* 1.3 59.9 + - - +
328A TYR* 5.0 5.4 - - + -
329A ASP* 3.6 0.5 - - - -
330A ASN* 2.9 54.1 + - + +
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Residues in contact with THR 307 (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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30A SER* 5.2 2.2 - - - +
32A TYR* 3.0 29.4 - - + +
115A ILE* 5.2 5.5 - - + +
289A VAL* 4.6 2.4 - - - +
290A GLY* 3.3 3.2 - - - -
291A MET* 2.8 51.7 + - - +
305A TRP* 3.7 22.0 + - + +
306A TRP* 1.3 74.1 - - - +
308A VAL* 1.3 64.9 + - - +
328A TYR* 3.3 9.2 - - - +
329A ASP* 2.7 30.1 - - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.0 6.5 + - - -
289A VAL 3.2 6.3 - - - +
290A GLY* 3.7 15.3 - - - -
307A THR* 1.3 81.9 - - - +
309A GLY* 1.3 60.0 + - - +
327A GLY* 3.6 0.2 - - - -
328A TYR* 2.8 51.8 + - + +
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Residues in contact with GLY 309 (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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32A TYR* 3.3 14.4 + - - -
114A MET* 3.9 5.6 - - - -
288A TYR* 3.3 2.8 - - - +
289A VAL 2.9 31.5 + - - +
308A VAL* 1.3 77.9 - - - +
310A ILE* 1.3 68.6 + - - +
326A ILE 3.0 14.1 - - - -
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Residues in contact with ILE 310 (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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114A MET* 3.7 2.7 - - - +
286A MET* 4.2 22.2 - - + -
287A MET 3.4 5.4 - - - +
288A TYR* 4.0 14.6 - - + -
309A GLY* 1.3 80.4 - - - +
311A ARG* 1.3 62.3 - - - +
312A PRO* 3.7 17.1 - - + +
325A GLU* 3.4 3.3 - - - +
326A ILE* 2.9 57.5 + - + +
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Residues in contact with ARG 311 (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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33A ARG* 3.8 19.0 - - - +
34A LEU* 3.7 24.8 - - - +
113A HIS* 3.3 30.7 + - - -
114A MET* 3.8 21.1 - - + +
286A MET* 3.3 3.1 - - - -
287A MET* 2.7 44.8 + - + +
310A ILE* 1.3 77.4 - - - +
312A PRO* 1.3 62.5 - - - +
323A VAL* 3.8 14.8 - - + +
324A MET 3.2 9.4 - - - +
325A GLU* 2.9 41.6 + - - -
357A ILE* 3.3 15.0 + - + +
360A ARG* 3.7 11.9 - - - +
364A ARG* 4.1 10.1 - - - +
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Residues in contact with PRO 312 (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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280A MET* 6.3 0.9 - - + -
284A TRP* 4.3 21.1 - - + -
285A ASP 3.4 7.2 - - - +
286A MET* 4.0 15.2 - - + -
310A ILE* 3.7 22.2 - - + +
311A ARG* 1.3 91.6 - - - +
313A MET* 1.3 60.0 + - - +
322A THR 4.2 0.5 - - - +
323A VAL* 3.7 2.8 - - - +
324A MET* 3.0 58.7 + - + +
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Residues in contact with MET 313 (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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283A ASN 3.3 1.2 - - - +
284A TRP* 3.3 11.9 - - - -
285A ASP* 2.6 42.7 + - + +
312A PRO* 1.3 74.0 - - - +
314A TYR* 1.3 61.2 + - - +
315A LYS* 3.9 14.6 + - + +
321A SER* 3.1 35.7 - - - +
322A THR 3.5 4.3 - - - +
323A VAL* 3.9 12.1 - - + -
350A GLN* 4.1 6.5 - - - +
352A GLN* 3.6 24.0 - - - +
355A ASP 4.8 1.6 - - - -
356A SER 3.7 11.9 - - - +
357A ILE* 3.5 44.4 - - + -
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Residues in contact with TYR 314 (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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283A ASN* 3.4 40.4 + - + -
284A TRP* 3.5 41.9 - + + -
312A PRO 4.3 0.4 - - - -
313A MET* 1.3 72.7 - - - +
315A LYS* 1.3 66.5 + - - +
316A TRP* 3.4 53.0 + + - -
321A SER* 3.2 5.2 - - - -
322A THR* 2.8 46.1 + - - +
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Residues in contact with LYS 315 (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 SER* 4.7 1.8 + - - -
282A ASP* 3.5 24.8 + - - +
283A ASN* 2.8 43.4 + - - +
284A TRP 4.3 0.7 - - - +
285A ASP* 3.1 39.6 + - - +
313A MET* 4.3 18.4 - - + +
314A TYR* 1.3 76.2 - - - +
316A TRP* 1.3 64.3 + - - +
317A THR 3.2 13.5 + - - +
320A MET 3.9 6.1 - - - -
321A SER* 4.1 2.2 - - - -
352A GLN* 6.0 0.7 - - - +
355A ASP* 2.6 41.8 + - + +
356A SER* 4.4 0.6 - - - +
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Residues in contact with TRP 316 (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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314A TYR* 3.7 40.2 - + - -
315A LYS* 1.3 73.6 - - - +
317A THR* 1.3 67.0 + - - +
320A MET* 3.2 20.9 + - + +
321A SER* 4.0 4.3 - - - -
322A THR* 2.8 37.8 + - + -
349A 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