Contacts of the strand formed by residues 277 - 282 (chain B) in PDB entry 3M0V
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 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B GLN* 4.2 8.5 + - - +
251B CYS 4.0 0.4 - - - -
253B VAL* 3.9 27.6 - - + -
268B VAL* 3.9 7.4 - - + -
271B LEU* 3.5 18.7 + - + -
272B ILE* 3.3 42.4 - - + +
275B GLY* 3.7 1.8 - - - -
276B LYS* 1.3 76.0 - - - +
278B GLY* 1.3 61.5 + - - +
279B GLY 4.4 6.3 - - - +
280B PHE* 3.8 31.2 - - + -
309B LEU* 3.9 6.5 - - + -
320B PHE* 4.0 11.1 - - + -
321B HIS 5.0 2.6 + - - -
322B PRO* 3.9 20.7 - - + +
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS* 5.3 0.7 + - - -
217B PHE* 3.5 26.1 - - - -
250B GLN* 3.4 28.0 - - - +
251B CYS 2.8 17.2 + - - -
276B LYS 3.1 5.5 + - - -
277B LEU* 1.3 72.8 - - - +
279B GLY* 1.3 54.6 + - - -
321B HIS 4.5 1.2 - - - +
322B PRO* 3.4 4.6 - - - +
323B ALA 3.0 17.8 + - - -
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Residues in contact with GLY 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B PHE* 5.5 0.2 - - - -
251B CYS 3.4 4.2 + - - +
252B LEU* 3.3 15.7 - - - +
253B VAL* 2.9 26.5 + - - +
277B LEU* 3.5 4.1 - - - +
278B GLY* 1.3 78.6 - - - +
280B PHE* 1.3 67.8 + - - -
322B PRO* 4.1 5.2 - - - -
323B ALA* 3.1 19.5 - - - -
325B MET* 5.1 0.2 - - - -
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Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LEU* 3.3 6.7 - - - +
253B VAL* 3.3 25.6 - - + -
255B LEU* 4.6 7.2 - - + -
268B VAL* 3.5 45.5 - - + -
277B LEU* 3.8 13.9 - - + -
279B GLY* 1.3 77.0 - - - -
281B HIS* 1.3 59.2 + - - +
282B PHE* 3.6 33.7 - + + -
305B VAL* 3.7 15.7 - - + -
309B LEU* 3.4 28.9 - - + -
322B PRO* 4.6 3.4 - - + -
323B ALA 3.0 9.0 + - - +
324B HIS* 4.0 17.5 - + - -
325B MET* 3.1 33.3 + - - +
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Residues in contact with HIS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TRP* 4.9 7.4 - + - -
127B ASN* 4.5 11.6 + - - -
177B THR* 4.5 6.0 - - + +
219B GLU* 2.9 13.4 + - - -
252B LEU* 3.6 21.3 - - + +
253B VAL 2.8 7.7 + - - -
254B ASP* 3.2 22.2 - - + +
255B LEU* 2.8 26.8 + - - +
280B PHE* 1.3 80.6 - - - +
282B PHE* 1.3 62.0 + - - +
283B ASN* 3.6 4.0 + - - -
325B MET* 3.3 23.1 - - + +
327B ASP* 3.0 16.4 + - + +
503B MN 2.0 33.7 + - - -
2002B RNS 3.1 12.8 - - - -
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 4.2 5.2 - - + -
255B LEU* 3.4 15.7 - - + -
280B PHE* 3.6 32.5 - + + -
281B HIS* 1.3 71.2 - - - +
283B ASN* 1.3 64.0 + - - +
294B ALA* 4.6 2.2 - - + -
302B LEU* 3.8 20.9 - - + -
305B VAL* 4.8 7.2 - - + -
306B PHE* 3.7 34.8 - + - -
309B LEU* 4.9 1.3 - - + -
324B HIS* 3.5 30.3 - + + -
325B MET 2.7 26.2 + - - +
326B ILE* 3.7 3.4 - - - -
327B ASP 3.0 20.8 + - - +
328B GLN* 3.6 7.9 - - - +
346B ILE* 3.6 34.5 - - + -
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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