Contacts of the strand formed by residues 271 - 278 (chain A) in PDB entry 5MJ3
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 LEU 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A PRO* 4.0 9.9 - - + -
258A TYR* 3.0 34.7 + - + -
259A PRO* 3.8 24.2 - - + -
262A TRP* 3.5 44.4 - - + +
270A SER* 1.3 72.8 - - - +
272A THR* 1.3 61.2 + - - +
273A PHE* 3.8 28.7 - - + -
292A ASP* 4.2 1.0 - - - +
310A ALA* 4.3 5.4 - - + -
311A GLN 3.4 24.9 - - - +
312A ASP* 3.9 0.9 - - - +
313A ARG* 3.0 29.0 + - - -
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Residues in contact with THR 272 (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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271A LEU* 1.3 72.9 - - - +
273A PHE* 1.3 69.1 + - - +
290A PHE* 5.3 3.7 - - + +
291A THR 3.3 11.2 + - - -
292A ASP* 2.7 23.4 + - - -
310A ALA* 3.4 4.5 - - - +
311A GLN* 2.8 56.0 + - + +
312A ASP 4.1 4.5 - - - +
313A ARG* 4.0 19.5 - - - +
319A TRP* 3.9 7.9 - - + -
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Residues in contact with PHE 273 (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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238A PRO* 4.2 9.6 - - + -
256A TRP* 3.4 44.6 - + + -
257A GLU 5.2 1.8 - - - -
258A TYR* 3.7 37.9 - + - -
259A PRO* 5.5 0.2 - - + -
271A LEU* 3.8 23.3 - - + -
272A THR* 1.3 79.0 + - - +
274A CYS* 1.3 60.2 + - - +
275A VAL 4.2 0.2 - - - -
290A PHE* 3.3 9.5 - - - +
291A THR* 2.8 39.3 + - + +
292A ASP 4.3 4.3 - - - -
293A LYS 3.3 23.1 - - - -
294A THR* 4.0 2.9 - - + -
308A VAL* 4.1 3.8 - - + -
309A ARG 3.2 9.0 - - - +
310A ALA* 3.6 25.4 - - + -
319A TRP* 4.2 4.3 - - - -
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Residues in contact with CYS 274 (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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273A PHE* 1.3 73.6 - - - +
275A VAL* 1.3 62.6 + - - +
288A ARG* 3.8 34.3 - - - -
289A VAL 3.4 6.3 - - - -
290A PHE* 3.7 29.8 - - + -
308A VAL* 3.1 6.4 - - - +
309A ARG* 2.9 41.2 + - + +
319A TRP* 3.9 13.4 - - + -
322A TRP* 3.7 16.7 - - - -
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Residues in contact with VAL 275 (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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254A VAL* 4.7 6.5 - - + -
256A TRP* 3.6 34.3 - - + -
274A CYS* 1.3 75.1 - - - +
276A GLN* 1.3 63.6 + - - +
277A VAL* 5.9 0.2 - - - -
287A ASP 3.9 0.5 - - - +
288A ARG* 3.2 3.3 - - - -
289A VAL* 2.8 51.0 + - + +
291A THR* 4.5 6.5 - - + -
296A ALA* 4.2 9.9 - - + -
298A VAL* 3.9 25.4 - - + +
306A ILE* 4.2 18.2 - - + -
307A SER 3.4 7.9 - - - +
308A VAL* 4.0 8.1 - - + -
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Residues in contact with GLN 276 (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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275A VAL* 1.3 76.3 - - - +
277A VAL* 1.3 72.8 + - - +
278A GLN* 3.9 17.9 + - + +
286A LYS* 5.2 4.5 - - - +
287A ASP 3.2 12.1 - - - +
288A ARG* 2.5 48.2 + - + +
305A SER 3.6 1.0 - - - +
306A ILE* 3.4 4.5 - - - +
307A SER* 2.8 40.4 + - - -
322A TRP* 3.8 32.4 - - + +
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Residues in contact with VAL 277 (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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275A VAL* 5.7 0.2 - - + -
276A GLN* 1.3 75.7 - - - +
278A GLN* 1.3 66.8 + - - +
285A LYS 5.3 1.2 - - - +
287A ASP* 3.0 32.4 + - + +
298A VAL* 4.0 30.3 - - + -
299A ILE 3.7 26.7 - - - +
300A CYS* 4.6 7.2 - - - -
301A ARG* 3.7 28.8 + - + +
304A ALA* 4.2 12.1 - - + -
305A SER 3.6 8.3 - - - +
306A ILE* 4.3 4.9 - - + -
327A CYS* 4.7 3.1 - - - -
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Residues in contact with GLN 278 (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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276A GLN* 3.9 25.5 + - + +
277A VAL* 1.3 78.4 - - - +
279A GLY* 1.3 59.5 + - - +
285A LYS 5.2 8.3 - - - +
286A LYS* 6.3 0.2 - - - -
301A ARG* 3.9 8.3 - - - +
304A ALA* 4.2 5.4 - - - -
305A SER* 2.9 34.4 + - - +
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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