Contacts of the strand formed by residues 320 - 333 (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 MET 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B TRP* 6.3 3.1 - - + -
316C TRP* 3.2 32.7 + - + +
317C THR* 3.1 36.2 + - + +
319C ILE* 1.3 80.4 - - + +
321C SER* 1.3 67.1 + - - +
349C GLN* 3.8 21.3 - - - +
350C GLN 3.4 9.0 - - - +
351C TRP* 3.8 34.5 - - + +
352C GLN* 4.7 0.2 - - - -
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Residues in contact with SER 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C MET* 3.1 30.7 - - - +
314C TYR 3.2 16.4 - - - -
315C LYS* 4.1 2.0 - - - -
316C TRP* 3.9 5.2 - - - -
320C MET* 1.3 78.2 - - - +
322C THR* 1.3 62.8 + - - +
323C VAL* 3.8 5.4 - - - +
349C GLN* 3.4 8.1 - - - -
350C GLN* 2.8 40.6 + - - -
352C GLN* 2.9 20.6 + - - -
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Residues in contact with THR 322 (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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312C PRO 4.2 0.5 - - - +
313C MET* 3.5 2.4 - - - +
314C TYR* 2.8 38.7 + - - +
316C TRP* 2.8 28.8 + - + -
321C SER* 1.3 70.7 - - - +
323C VAL* 1.3 63.2 + - - +
324C MET* 4.4 0.6 + - + -
347C LEU* 4.0 22.4 - - + -
348C ALA 3.4 9.2 - - - +
349C GLN* 2.5 22.6 + - - +
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Residues in contact with VAL 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.0 17.9 - - + +
311C ARG* 3.8 25.6 - - + +
312C PRO 3.7 12.1 - - - +
313C MET* 3.9 13.9 - - + -
321C SER* 3.8 17.0 - - - +
322C THR* 1.3 79.9 - - - +
324C MET* 1.3 63.7 + - - +
347C LEU* 3.6 3.3 - - - +
348C ALA* 2.6 48.1 + - + +
350C GLN* 4.0 28.0 - - + +
357C ILE* 5.3 2.7 - - + -
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Residues in contact with MET 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.6 0.7 - - - -
311C ARG* 3.2 10.6 - - - +
312C PRO* 3.1 45.3 + - + +
322C THR* 5.8 0.9 - - + -
323C VAL* 1.3 77.6 - - - +
325C GLU* 1.3 65.6 + - - +
326C ILE* 4.1 28.5 - - + -
345C ILE* 5.2 9.2 - - + -
346C THR 3.1 10.5 - - - +
347C LEU* 3.9 26.5 - - + -
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Residues in contact with GLU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 3.4 22.1 - - + +
33C ARG 4.3 0.7 - - - -
34C LEU* 3.0 29.1 + - + +
114C MET* 3.7 18.4 - - + +
310C ILE 3.5 10.5 - - - +
311C ARG* 2.9 35.7 + - - -
324C MET* 1.3 76.7 - - - +
326C ILE* 1.3 66.2 + - - +
344C LYS* 2.6 33.6 + - - +
345C ILE* 3.4 3.1 - - - -
346C THR* 2.8 41.1 + - - +
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Residues in contact with ILE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLY* 3.0 3.8 - - - -
310C ILE* 2.9 56.2 + - + +
312C PRO* 6.2 0.2 - - + -
324C MET* 4.1 27.4 - - + -
325C GLU* 1.3 82.6 - - - +
327C GLY* 1.3 63.5 - - - +
328C TYR* 6.3 0.9 - - + -
343C TYR* 5.9 4.3 - - + -
344C LYS 3.3 9.0 - - - +
345C ILE* 4.4 20.2 - - + -
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Residues in contact with GLY 327 (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* 3.7 30.7 - - - +
308C VAL 3.6 7.4 - - - -
325C GLU 4.2 0.2 - - - -
326C ILE* 1.3 78.4 - - - +
328C TYR* 1.3 61.2 + - - -
329C ASP* 5.2 0.7 - - - +
342C GLN 3.8 0.5 - - - +
343C TYR* 3.2 4.8 - - - +
344C LYS* 2.7 40.8 + - - +
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Residues in contact with TYR 328 (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* 3.8 1.0 - - - -
306C TRP* 5.0 6.3 - - + -
307C THR* 3.3 9.5 - - - +
308C VAL* 2.8 51.4 + - + +
326C ILE* 6.3 0.7 - - + -
327C GLY* 1.3 74.6 - - - +
329C ASP* 1.3 73.2 - - - +
330C ASN* 3.3 37.8 + - + +
341C ASN* 4.0 15.8 - - + +
342C GLN 3.3 15.5 - - - -
343C TYR* 4.2 13.9 - + + -
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Residues in contact with ASP 329 (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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24C GLN* 5.9 0.2 - - - -
25C THR* 3.3 34.4 + - + +
28C ALA* 4.2 3.4 - - - +
30C SER* 4.6 7.1 + - - +
31C LYS* 5.1 2.3 - - - -
32C TYR* 4.0 14.8 + - - -
305C TRP* 3.3 17.7 + - - +
306C TRP 3.6 3.1 - - - -
307C THR* 2.7 28.9 - - - +
327C GLY 5.2 0.5 - - - +
328C TYR* 1.3 81.7 - - - +
330C ASN* 1.3 61.3 + - - +
340C ASN 4.4 0.2 - - - -
341C ASN* 3.1 7.4 - - - +
342C GLN* 2.8 42.5 + - - +
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Residues in contact with ASN 330 (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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304C LYS 3.8 0.9 - - - +
305C TRP* 3.5 2.3 - - - -
306C TRP* 2.9 50.8 + - + +
328C TYR* 3.3 30.6 + - + +
329C ASP* 1.3 74.2 - - - +
331C VAL* 1.3 69.0 + - - +
332C GLU* 4.4 1.9 + - - +
339C LYS* 3.7 35.7 - - - +
340C ASN 3.3 3.9 + - - -
341C ASN* 3.7 14.1 + - - +
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 3.6 17.9 - - + -
26C THR 3.9 7.2 - - - +
27C GLY* 3.8 18.8 - - - +
28C ALA* 3.6 23.3 - - + +
303C THR* 4.0 14.8 - - - -
304C LYS 3.5 8.5 - - - +
305C TRP* 3.7 20.4 - - + -
329C ASP* 5.1 0.2 - - + -
330C ASN* 1.3 81.2 + - - +
332C GLU* 1.3 62.6 + - - +
339C LYS* 3.2 0.7 - - - -
340C ASN* 2.7 40.7 + - + +
376C TRP* 3.2 20.0 + - + -
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Residues in contact with GLU 332 (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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303C THR* 3.4 4.2 - - - -
304C LYS* 2.8 65.6 + - + +
330C ASN* 4.2 2.2 + - - +
331C VAL* 1.3 76.3 - - - +
333C SER* 1.3 75.8 + - - +
334C GLN* 3.5 1.9 + - - -
337C GLY* 3.9 11.1 - - - +
338C ASP 3.2 12.3 - - - +
339C LYS* 2.6 40.2 + - + +
376C TRP* 4.2 0.7 - - - -
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Residues in contact with SER 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C GLY 4.1 5.0 + - - -
332C GLU* 1.3 76.9 - - - +
334C GLN* 1.3 62.5 + - - +
335C ARG 3.0 13.9 + - - -
336C THR* 3.3 21.7 + - - -
337C GLY* 3.0 22.9 + - - -
338C ASP 3.0 8.0 + - - -
376C TRP* 3.5 33.9 - - - +
393C ALA* 3.2 22.0 - - - +
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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