Contacts of the strand formed by residues 272 - 277 (chain A) in PDB entry 3DYD
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 ILE 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LEU* 4.1 3.8 - - + -
244A ILE* 3.3 22.2 - - + +
246A ALA* 3.8 14.4 - - + -
263A LEU* 3.6 23.6 - - + +
264A ALA* 3.7 28.0 - - + +
267A SER* 3.9 16.4 - - - -
270A VAL* 3.6 8.1 - - + +
271A PRO* 1.3 80.1 - - - +
273A LEU* 1.3 62.5 + - - +
274A SER* 3.5 22.7 - - - +
293A LEU 3.6 0.9 - - - +
294A ILE 3.8 0.2 - - - -
295A HIS* 2.8 48.2 + - + +
301A PHE* 3.8 6.9 - - - -
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Residues in contact with LEU 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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151A CYS* 3.8 34.5 - - + +
154A VAL* 4.4 8.1 - - + -
155A LEU* 3.7 32.8 - - + -
244A ILE 3.0 7.3 + - - +
245A LEU* 3.4 11.7 - - + +
246A ALA 2.9 23.7 + - - -
272A ILE* 1.3 71.9 - - - +
274A SER* 1.3 60.2 + - - +
275A CYS* 4.9 0.4 - - - -
292A ILE* 4.4 5.4 - - + -
293A LEU 3.6 2.2 - - - -
294A ILE* 3.8 31.6 - - + -
301A PHE* 3.6 29.8 - - + -
305A ILE* 4.9 3.6 - - + -
309A LEU* 4.4 9.2 - - + -
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Residues in contact with SER 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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246A ALA* 3.3 6.6 - - - +
248A GLU* 3.6 23.7 + - - -
264A ALA* 4.7 3.3 + - - +
272A ILE* 3.5 13.0 - - - +
273A LEU* 1.3 71.9 - - - +
275A CYS* 1.3 62.8 + - - +
276A GLY 4.1 0.3 + - - -
291A TRP 3.6 0.9 - - - +
292A ILE* 3.4 3.7 - - - -
293A LEU* 2.7 55.6 + - - +
295A HIS* 3.3 24.6 + - - -
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Residues in contact with CYS 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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144A CYS* 3.7 18.8 - - - -
147A ALA* 3.8 8.7 - - + -
148A ILE* 3.8 23.3 - - + -
151A CYS* 3.5 21.8 - - - -
245A LEU* 3.4 28.7 - - + -
246A ALA 2.7 12.9 + - - +
247A ASP* 3.7 3.4 - - - +
248A GLU* 2.7 34.3 + - - +
249A ILE 3.4 1.2 + - - -
274A SER* 1.3 75.7 - - - +
276A GLY* 1.3 57.5 + - - +
291A TRP 3.4 3.1 - - - -
292A ILE* 4.5 1.3 - - - -
293A LEU* 5.9 0.4 - - - -
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Residues in contact with GLY 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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144A CYS* 3.4 14.1 - - - +
248A GLU* 4.0 13.9 - - - -
249A ILE* 3.7 8.7 - - - -
274A SER 4.1 0.2 + - - -
275A CYS* 1.3 74.8 - - - +
277A GLY* 1.3 58.7 + - - -
290A GLY* 3.4 4.3 - - - -
291A TRP* 3.1 39.3 + - - +
293A LEU* 5.6 0.9 - - - +
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Residues in contact with GLY 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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126A TYR* 5.2 0.2 + - - -
144A CYS* 5.1 0.2 - - - -
249A ILE* 3.5 18.7 - - - +
276A GLY* 1.3 73.9 - - - -
278A LEU* 1.3 63.9 + - - -
279A ALA 3.4 2.6 + - - -
280A LYS 4.9 0.5 + - - -
281A ARG* 5.0 1.4 - - - +
282A TRP* 3.7 13.7 - - - -
289A LEU 3.7 0.7 - - - -
290A GLY* 3.7 13.5 - - - -
291A TRP* 3.3 26.9 - - - -
500A PLP 5.6 0.2 - - - -
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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