Contacts of the strand formed by residues 306 - 311 (chain A) in PDB entry 4BWM
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 PHE 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLY 4.2 0.9 - - - -
305A ALA* 1.3 75.8 - - - +
307A VAL* 1.3 60.9 + - - +
326A ALA* 3.1 3.9 - - - -
327A ALA 2.7 39.8 + - - +
328A ARG* 5.8 2.2 - - - -
349A ARG* 3.2 63.9 - - + +
350A GLY* 4.2 5.2 - - - -
371A ASP* 4.8 1.1 - - + -
373A PRO* 5.5 0.9 - - + -
406A ALA* 3.4 20.5 - - - +
409A SER* 4.0 12.3 - - - -
410A GLU* 3.6 34.1 - - + +
413A PHE* 3.6 44.4 - + + -
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Residues in contact with VAL 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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305A ALA 3.9 2.1 + - - +
306A PHE* 1.3 74.2 - - - +
308A GLY* 1.3 63.9 + - - +
309A PHE* 4.8 7.9 - - + -
324A LEU* 3.4 28.3 - - + -
325A ALA 3.3 12.3 - - - +
326A ALA* 4.3 4.0 - - + +
345A LEU* 4.1 15.0 - - + -
347A GLU 5.6 0.7 - - - +
348A ALA* 4.3 4.7 - - + -
349A ARG 2.7 37.7 + - - +
350A GLY* 4.1 5.1 - - - +
351A LEU 4.6 2.6 + - - +
353A ALA* 5.7 1.3 - - - -
356A LEU* 3.8 22.4 - - + -
406A ALA* 3.8 3.2 - - - -
409A SER* 3.6 18.2 + - - -
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Residues in contact with GLY 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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307A VAL* 1.3 75.8 - - - +
309A PHE* 1.3 66.8 + - - +
324A LEU* 3.5 0.9 - - - -
325A ALA 2.8 31.6 + - - +
402A ALA* 3.5 23.5 - - - +
405A ARG* 4.1 6.5 - - - -
406A ALA* 3.4 11.1 - - - +
409A SER* 5.3 0.2 - - - -
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Residues in contact with PHE 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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307A VAL* 4.8 5.6 - - + -
308A GLY* 1.3 80.6 - - - +
310A VAL* 1.3 63.9 + - - +
311A LEU* 3.7 40.6 - - + -
321A LEU* 3.8 10.3 - - + -
323A ALA 3.3 12.6 - - - +
324A LEU* 4.1 7.9 - - + -
351A LEU 3.5 21.5 - - - -
352A LEU* 3.3 34.8 - - + -
353A ALA* 4.8 1.3 - - - -
355A ASP* 4.2 3.6 - - + -
356A LEU* 3.7 42.0 - - + -
398A TRP* 5.2 2.5 - + - -
402A ALA* 4.1 3.8 - - - +
405A ARG* 2.9 27.0 + - - +
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Residues in contact with VAL 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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309A PHE* 1.3 79.1 - - - +
311A LEU* 1.3 73.1 + - - +
321A LEU* 3.7 4.2 - - - +
322A LEU* 2.9 46.8 + - + +
323A ALA* 3.1 14.3 + - + +
400A GLU* 3.4 34.8 - - + +
401A GLU 3.9 1.1 - - - -
402A ALA* 3.5 24.5 - - + +
405A ARG* 3.7 17.7 - - - +
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Residues in contact with LEU 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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309A PHE* 3.7 35.4 - - + -
310A VAL* 1.3 86.8 - - - +
312A SER* 1.3 65.2 + - - +
313A ARG* 3.2 22.6 + - - +
314A LYS* 4.1 10.5 - - - +
316A PRO* 4.0 26.2 - - + -
319A ALA* 3.8 2.9 - - + -
320A ASP 3.5 4.5 - - - +
321A LEU* 4.1 6.1 - - + -
322A LEU* 4.1 4.3 - - - +
355A ASP* 4.8 5.6 - - + +
356A LEU* 5.5 0.4 - - + -
359A LEU* 3.9 28.9 - - + -
405A ARG* 4.6 3.2 - - - +
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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