Contacts of the strand formed by residues 303 - 316 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B GLY 4.3 10.2 + - - +
293B GLN* 3.9 3.8 + - - +
294B ASP* 3.6 1.7 - - - +
295B ILE* 2.6 56.3 + - - +
301B ASN 4.8 0.2 - - - +
302B GLY* 1.3 82.8 - - - +
304B LYS* 1.3 60.1 + - - +
305B TRP* 4.2 3.9 - - - +
331B VAL* 4.0 22.7 - - + -
332B GLU 3.4 9.0 - - - +
334B GLN* 4.3 3.4 - - - +
376B TRP* 4.1 10.3 - - + -
378B TYR* 3.6 23.8 - - - +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 3.4 40.6 + - + +
293B GLN 3.4 2.9 - - - +
294B ASP* 3.8 19.0 + - - +
303B THR* 1.3 75.8 - - - +
305B TRP* 1.3 60.1 + - - +
306B TRP* 4.9 9.4 - - + +
330B ASN* 3.7 1.7 - - - +
331B VAL* 3.5 2.1 - - - -
332B GLU* 2.9 61.5 + - + +
334B GLN* 6.5 0.2 - - - -
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY 5.0 2.9 - - - +
28B ALA* 3.5 16.1 - - + +
29B GLN* 3.4 40.4 - - + -
30B SER* 3.3 29.6 - - - -
117B PHE* 4.2 3.8 - + - -
291B MET* 3.7 24.5 - - + +
292B TYR* 3.4 3.7 - - - -
293B GLN* 2.7 75.4 + - + +
303B THR* 5.2 3.6 - - - +
304B LYS* 1.3 76.6 - - - +
306B TRP* 1.3 73.6 + - - +
307B THR* 3.8 18.8 + - - -
329B ASP* 3.3 21.4 + - - -
330B ASN 3.5 2.7 - - - -
331B VAL* 3.7 28.5 - - + -
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Residues in contact with TRP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B MET 3.4 9.2 - - - -
292B TYR* 3.4 50.1 - + + -
304B LYS* 4.9 9.5 - - + +
305B TRP* 1.3 81.2 - - - +
307B THR* 1.3 61.4 + - - +
308B VAL* 6.6 0.7 - - + -
328B TYR* 4.1 5.6 - - + +
329B ASP* 3.6 0.9 - - - -
330B ASN* 3.0 54.2 + - + +
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 5.2 2.2 - - - +
32B TYR* 3.0 29.2 - - + +
115B ILE* 5.1 6.1 - - + +
289B VAL* 5.9 1.6 - - - -
290B GLY* 3.2 2.8 - - - -
291B MET* 2.8 55.1 + - - +
305B TRP* 3.8 21.3 + - + +
306B TRP* 1.3 73.9 - - - +
308B VAL* 1.3 65.8 + - - +
328B TYR* 3.2 10.1 - - - +
329B ASP* 2.7 30.3 - - - +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.0 5.5 + - - -
289B VAL 3.2 6.5 - - - +
290B GLY* 3.7 15.0 - - - -
306B TRP* 6.6 0.7 - - + -
307B THR* 1.3 83.6 - - - +
309B GLY* 1.3 61.1 - - - +
328B TYR* 2.8 51.0 + - + +
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 3.3 14.1 + - - -
114B MET* 3.9 6.1 - - - -
288B TYR* 3.3 2.8 - - - +
289B VAL 2.8 32.8 + - - +
308B VAL* 1.3 77.2 - - - +
310B ILE* 1.3 67.7 + - - +
326B ILE 3.0 14.4 - - - -
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B MET* 3.6 3.3 - - - +
286B MET* 4.3 21.1 - - + -
287B MET 3.4 6.7 - - - +
288B TYR* 4.0 14.8 - - + -
309B GLY* 1.3 80.3 - - - +
311B ARG* 1.3 62.0 - - - +
312B PRO* 3.7 17.7 - - + +
325B GLU* 3.5 3.5 - - - +
326B ILE* 2.9 52.5 + - + +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 3.8 19.0 - - - +
34B LEU* 3.7 24.1 - - - +
113B HIS* 3.3 31.2 + - - -
114B MET* 3.7 21.0 - - + +
286B MET* 3.3 2.5 - - - -
287B MET* 2.7 45.8 + - + +
310B ILE* 1.3 75.5 - - - +
312B PRO* 1.3 63.1 - - - +
323B VAL* 3.8 15.9 - - + +
324B MET 3.2 10.1 - - - +
325B GLU* 2.9 34.0 + - - +
357B ILE* 3.3 14.9 + - + +
360B ARG* 3.7 11.5 - - - +
364B ARG* 4.0 11.3 - - - +
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Residues in contact with PRO 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B MET* 6.2 0.9 - - + -
284B TRP* 4.3 21.1 - - + -
285B ASP 3.4 7.2 - - - +
286B MET* 4.0 15.0 - - + -
310B ILE* 3.7 23.1 - - + +
311B ARG* 1.3 89.9 - - - +
313B MET* 1.3 60.0 + - - +
314B TYR 4.3 0.2 - - - -
322B THR 4.2 0.3 - - - +
323B VAL* 3.7 3.0 - - - +
324B MET* 3.1 57.1 + - + +
326B ILE* 6.0 0.2 - - + -
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B ASN 3.4 0.9 - - - +
284B TRP* 3.3 11.6 - - - -
285B ASP* 2.6 40.9 + - + +
312B PRO* 1.3 76.0 - - - +
314B TYR* 1.3 61.7 + - - +
315B LYS* 3.9 15.7 + - + +
321B SER* 3.1 34.5 - - - +
322B THR 3.5 3.1 - - - -
323B VAL* 3.9 14.4 - - + +
350B GLN* 4.1 5.4 - - - +
352B GLN* 3.6 24.2 - - - +
355B ASP 4.7 1.8 - - - +
356B SER 3.7 12.3 - - - +
357B ILE* 3.5 43.1 - - + -
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Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B ASN* 3.4 40.6 + - + -
284B TRP* 3.5 41.8 - + + -
312B PRO 4.3 0.2 - - - -
313B MET* 1.3 72.7 - - - +
315B LYS* 1.3 66.8 + - - +
316B TRP* 3.5 52.1 + + - -
321B SER* 3.2 5.0 - - - -
322B THR* 2.8 47.0 + - + +
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Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B SER* 4.7 1.8 + - - -
282B ASP* 3.5 24.8 + - - +
283B ASN* 2.8 36.9 + - - +
284B TRP 4.3 0.9 - - - +
285B ASP* 3.1 45.6 + - - +
313B MET* 4.3 17.7 - - + +
314B TYR* 1.3 76.8 + - - +
316B TRP* 1.3 63.3 + - - +
317B THR 3.2 14.0 + - - +
318B PRO* 5.8 0.2 - - + -
320B MET 3.9 5.6 - - - -
321B SER* 4.1 1.8 - - - -
352B GLN* 6.0 0.2 - - - +
355B ASP* 2.6 42.3 + - + +
356B SER* 4.4 0.4 - - - +
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Residues in contact with TRP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B TYR* 3.7 34.4 - + + -
315B LYS* 1.3 73.9 - - - +
317B THR* 1.3 66.0 + - - +
320B MET* 3.2 20.6 + - + +
321B SER* 3.9 4.5 - - - -
322B THR* 2.8 43.9 + - + -
349B GLN* 3.9 12.9 + - - -
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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
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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