Contacts of the strand formed by residues 305 - 312 (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 SER 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLN 3.6 1.6 - - - +
277A VAL* 3.6 4.9 - - - +
278A GLN 2.9 33.8 + - - +
303A ASN 4.0 2.1 + - - -
304A ALA* 1.3 75.7 - - - +
306A ILE* 1.3 66.1 + - - +
307A SER* 4.0 12.4 + - - -
324A SER* 4.7 7.8 - - - -
325A VAL 3.5 10.1 + - - -
326A PRO* 3.7 20.3 - - - +
327A CYS* 4.4 1.3 - - - -
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Residues in contact with ILE 306 (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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241A LEU* 3.8 2.0 - - + +
243A LEU* 3.4 28.0 - - + -
252A VAL* 4.3 3.8 - - + -
254A VAL* 3.7 29.6 - - + -
275A VAL* 4.2 13.7 - - + -
276A GLN 3.4 3.1 - - - +
277A VAL* 4.3 8.5 - - + -
298A VAL* 3.3 29.8 - - + -
300A CYS* 3.4 31.4 - - - -
305A SER* 1.3 74.7 - - - +
307A SER* 1.3 61.4 + - - +
308A VAL* 4.5 3.4 - - + -
324A SER* 3.3 2.3 - - - -
325A VAL* 2.9 36.4 + - + +
327A CYS* 4.1 1.9 - - - -
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Residues in contact with SER 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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275A VAL* 3.4 0.7 - - - +
276A GLN* 2.8 45.0 + - - -
305A SER* 4.4 8.0 + - - -
306A ILE* 1.3 73.7 - - - +
308A VAL* 1.3 67.6 + - - +
322A TRP* 3.4 26.5 - - - +
323A ALA 3.1 4.5 - - - -
324A SER* 2.6 25.3 + - - -
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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
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238A PRO* 3.6 24.3 - - + +
241A LEU* 3.8 30.3 - - + -
254A VAL* 4.3 2.2 - - + -
256A TRP* 3.9 32.8 - - + -
273A PHE* 4.1 4.3 - - + -
274A CYS 3.1 11.0 - - - +
275A VAL* 4.0 20.4 - - + -
306A ILE* 4.5 1.3 - - + -
307A SER* 1.3 81.0 - - - +
309A ARG* 1.3 68.6 + - - +
322A TRP* 3.5 2.4 - - - -
323A ALA* 2.8 32.0 + - - +
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Residues in contact with ARG 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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238A PRO* 4.0 4.3 - - - -
273A PHE* 3.2 6.4 - - - +
274A CYS* 2.9 39.5 + - + +
288A ARG* 3.7 26.7 - - - +
308A VAL* 1.3 74.9 - - - +
310A ALA* 1.3 60.9 + - - +
319A TRP* 3.6 45.8 - - + +
320A SER* 3.4 31.6 + - - +
321A GLU 3.9 3.4 - - - +
322A TRP* 3.4 48.8 - - + +
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Residues in contact with ALA 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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235A PRO* 3.9 10.5 - - + +
236A ASP 4.5 2.2 - - - +
238A PRO* 4.3 7.9 - - + -
259A PRO* 5.5 0.9 - - + -
271A LEU* 4.3 13.9 - - + -
272A THR 3.4 5.6 - - - +
273A PHE* 3.6 24.2 - - + -
309A ARG* 1.3 74.8 - - - +
311A GLN* 1.3 61.7 + - - +
319A TRP* 3.4 6.9 - - - -
320A SER* 2.7 46.0 + - - +
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Residues in contact with GLN 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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235A PRO* 4.3 4.0 - - - -
271A LEU* 3.4 8.7 - - - +
272A THR* 2.8 34.7 + - + +
310A ALA* 1.3 75.5 - - - +
312A ASP* 1.3 81.5 + - - +
313A ARG 3.2 0.2 + - - -
315A TYR 4.3 3.6 - - - +
316A SER* 3.9 21.5 + - - +
317A SER 2.8 29.5 + - - +
318A SER 4.3 4.5 - - - +
319A TRP* 3.5 50.7 - - + +
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Residues in contact with ASP 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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136A TYR* 2.8 31.6 + - - +
233A ILE* 4.9 1.1 - - + -
235A PRO* 4.4 5.1 - - - +
262A TRP* 3.7 14.2 - - + -
269A PHE 5.7 0.2 - - - -
270A SER 4.3 3.2 - - - +
271A LEU* 3.9 11.5 - - - +
272A THR* 4.1 0.9 - - - +
311A GLN* 1.3 85.5 - - - +
313A ARG* 1.3 65.5 + - - +
314A TYR* 2.8 27.2 + - - +
315A TYR* 3.1 25.9 + - - +
317A SER* 4.0 13.4 + - - +
178B ARG* 3.0 26.4 + - - -
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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