Contacts of the strand formed by residues 249 - 254 (chain A) in PDB entry 3THP
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ILE* 5.6 0.7 - - - -
240A ASP* 3.1 34.5 - - + +
245A PHE* 4.6 5.2 - - + -
246A GLU 4.6 2.7 - - - +
247A ASP 3.4 9.4 + - - +
248A GLU* 1.3 79.6 - - - +
250A VAL* 1.3 70.1 + - - +
251A SER* 5.5 0.9 - - - +
280A LEU 3.8 0.2 - - - +
281A VAL* 3.7 0.3 - - - +
282A MSE 3.0 61.3 + - + +
287A ARG* 4.4 12.3 - - - +
332A THR* 4.2 19.5 - - + -
333A PHE 3.8 10.5 - - - +
334A ARG* 4.2 22.9 - - + -
335A LYS 5.5 0.2 - - - +
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Residues in contact with VAL 250 (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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208A LEU* 6.2 1.1 - - + -
211A TRP* 5.7 4.5 - - + -
217A ILE* 3.7 34.3 - - + -
221A PRO* 5.5 1.3 - - + -
248A GLU* 4.9 0.2 - - + -
249A ILE* 1.3 83.1 - - - +
251A SER* 1.3 59.4 + - - +
279A LEU* 3.6 17.5 - - + -
280A LEU 3.1 3.1 - - - +
281A VAL* 3.5 35.2 - - + -
331A PHE 3.7 0.4 - - - +
332A THR* 3.4 3.3 - - - +
333A PHE* 2.7 62.6 + - + +
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Residues in contact with SER 251 (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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249A ILE* 5.8 0.4 - - - -
250A VAL* 1.3 72.1 - - - +
252A LEU* 1.3 60.7 + - - +
253A SER* 3.7 2.5 + - - -
278A SER 3.7 1.7 - - - +
279A LEU* 3.5 3.8 - - - -
280A LEU* 2.7 53.1 + - - +
328A ARG* 5.8 1.3 - - - -
330A SER* 5.0 2.4 - - - -
331A PHE 3.2 3.7 + - - -
332A THR* 3.0 37.6 + - - +
403A AKG 3.4 24.5 - - - +
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Residues in contact with LEU 252 (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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143A ILE* 3.6 31.2 - - + -
144A ILE* 4.5 11.7 - - + -
152A LEU* 3.6 31.4 - - + -
207A PHE* 6.1 1.6 - - + -
211A TRP* 5.5 10.5 - - + +
251A SER* 1.3 68.3 - - - +
253A SER* 1.3 59.9 + - - +
254A LEU* 3.5 17.2 - - + +
277A ARG* 4.4 7.4 - - - -
278A SER 3.7 9.4 - - - +
279A LEU* 4.1 11.8 - - + +
330A SER* 3.3 3.2 - - - -
331A PHE* 2.8 52.2 + - + +
333A PHE* 4.6 10.5 - - + -
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Residues in contact with SER 253 (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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251A SER 3.7 3.4 + - - -
252A LEU* 1.3 73.8 - - - +
254A LEU* 1.3 60.6 + - - +
256A SER 5.6 2.5 - - - -
274A LEU* 4.1 10.5 + - - +
275A PRO 3.3 6.4 + - - -
276A ARG* 3.7 3.4 - - - -
277A ARG* 3.0 25.8 + - - -
278A SER* 3.1 26.8 + - - -
280A LEU* 6.1 0.9 - - - +
328A ARG* 3.2 39.7 + - - -
329A THR 3.7 3.4 - - - -
330A SER* 4.3 1.1 - - - +
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Residues in contact with LEU 254 (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 ILE* 4.2 13.7 - - + -
149A GLU* 3.9 21.5 - - + +
152A LEU* 3.7 41.7 - - + -
153A LEU* 4.1 11.9 - - + +
252A LEU* 3.5 21.3 - - + +
253A SER* 1.3 77.0 - - - +
255A GLY* 1.3 61.7 + - - +
256A SER 3.6 3.3 + - - -
276A ARG* 4.7 1.6 - - - -
277A ARG 4.5 3.1 - - - +
328A ARG* 3.6 6.6 - - - +
329A THR* 2.8 46.1 + - + +
331A PHE* 3.6 26.2 - - + -
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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