Contacts of the strand formed by residues 306 - 313 (chain A) in PDB entry 1L0N
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 SER 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A TYR 3.2 13.5 - - - -
281A ASP* 3.9 6.1 - - - +
304A CYS* 3.4 10.2 - - - -
305A GLN* 1.3 83.5 - - - +
307A PHE* 1.3 64.4 + - - +
308A GLN* 6.0 0.7 - - - +
323A HIS* 5.0 2.6 + - - -
324A PHE* 3.4 2.1 - - - +
325A VAL* 3.0 46.7 + - - +
20I ARG* 5.3 0.4 - - - -
43I LEU* 3.7 6.0 - - - +
47I ARG 3.5 19.7 - - - -
48I SER* 4.2 5.6 + - - -
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Residues in contact with PHE 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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277A ILE* 3.8 13.5 - - + -
278A GLY 3.5 20.6 - - - -
279A HIS* 3.4 7.3 - - - +
280A TYR* 2.8 59.9 + + + +
294A LEU* 3.4 39.9 - - + -
295A ALA* 3.7 18.6 - - + -
298A ALA* 4.4 1.6 - - + -
304A CYS* 4.0 5.6 - - - -
306A SER* 1.3 77.0 - - - +
308A GLN* 1.3 73.6 + - - +
309A THR* 5.0 1.8 - - + -
322A ALA* 5.5 3.8 - - + -
323A HIS* 3.2 8.5 - - - +
324A PHE* 3.5 18.4 - - + +
334A MET* 3.6 21.8 - - + -
338A LEU* 5.8 0.4 - - + -
20I ARG* 3.8 1.6 + - - -
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Residues in contact with GLN 308 (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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146A ARG* 2.8 39.2 - - - +
150A PHE* 4.4 4.4 - - - -
279A HIS* 4.0 11.7 - - + -
306A SER* 6.0 0.4 - - - +
307A PHE* 1.3 82.6 - - - +
309A THR* 1.3 64.6 + - - +
310A PHE* 4.2 2.7 - - - +
322A ALA* 3.2 2.3 - - - -
323A HIS* 2.8 60.7 + - + +
20I ARG* 4.7 10.3 - - - +
52I ARG* 2.6 45.6 + - - +
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Residues in contact with THR 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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274A ASN* 3.6 31.7 + - - +
277A ILE* 3.7 32.3 - - + -
278A GLY* 3.2 23.5 + - - +
279A HIS* 4.9 2.0 - - - +
307A PHE* 4.8 2.5 - - + -
308A GLN* 1.3 73.3 - - - +
310A PHE* 1.3 55.0 + - - +
321A GLY 3.3 9.6 - - - -
322A ALA* 3.9 10.5 - - + -
338A LEU* 5.6 0.2 - - + -
342A TRP* 6.0 1.6 - - - +
52I ARG* 2.4 35.0 + - - +
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Residues in contact with PHE 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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150A PHE* 3.5 38.4 - + + -
153A LEU* 4.1 10.1 - - + -
254A ALA* 5.0 0.7 - - + -
255A ILE 4.1 0.4 - - - -
256A ALA* 3.8 17.0 - - + -
271A GLN* 6.1 0.4 - - - +
274A ASN* 3.1 10.9 - - - +
308A GLN* 4.2 6.3 - - - -
309A THR* 1.3 76.2 - - - +
311A ASN* 1.3 61.0 + - - +
312A ILE* 3.9 18.6 - - + -
319A LEU* 3.5 26.9 - - + -
320A LEU* 3.4 0.3 - - - +
321A GLY 2.7 52.3 + - - +
322A ALA* 3.5 30.5 - - - -
323A HIS* 4.0 0.7 - - + -
52I ARG* 4.1 17.0 - - - +
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Residues in contact with ASN 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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259A GLY* 5.4 0.9 - - - -
260A PRO* 4.9 4.5 - - - +
267A ASN* 2.9 32.3 + - - +
270A LEU* 4.4 11.3 - - + +
271A GLN* 3.1 44.6 + - - +
274A ASN* 4.1 2.9 - - - +
310A PHE* 1.3 75.0 - - - +
312A ILE* 1.3 64.9 + - - +
313A CYS* 3.7 14.0 + - - -
319A LEU 3.6 3.5 - - - -
320A LEU* 3.9 22.0 - - + +
55I LEU* 6.2 0.8 - - - +
57I GLY 5.3 2.0 - - - -
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Residues in contact with ILE 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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150A PHE* 4.3 23.3 - - + -
154A HIS* 4.5 13.0 - - + +
259A GLY* 5.7 0.3 - - - -
260A PRO 5.0 0.7 - - - +
310A PHE* 3.9 27.6 - - + -
311A ASN* 1.3 77.3 - - - +
313A CYS* 1.3 65.4 + - - +
314A TYR* 3.9 32.8 - - + +
318A GLY* 3.3 6.2 - - - -
319A LEU* 2.9 37.2 + - + +
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Residues in contact with CYS 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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260A PRO 4.7 4.3 - - - -
261A GLY 4.5 0.2 - - - -
262A TRP* 3.0 57.9 + - + +
267A ASN* 3.8 30.7 - - - -
311A ASN* 3.7 16.6 + - - -
312A ILE* 1.3 81.2 - - - +
314A TYR* 1.3 74.5 + - - +
317A THR 4.1 2.7 - - - -
57I GLY 5.8 5.2 - - - -
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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
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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