Contacts of the strand formed by residues 302 - 306 (chain A) in PDB entry 1T9A
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 PRO 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ILE* 5.7 0.4 - - + +
299A ALA* 3.9 17.7 - - + -
300A LYS 3.4 7.4 - - - +
301A LYS* 1.3 90.8 - - - +
303A VAL* 1.3 59.5 + - - +
329A ILE* 3.9 25.8 - - + -
330A PRO* 3.2 12.6 - - - +
368A ASP* 3.5 2.2 - - - +
369A LEU* 3.4 11.9 - - + +
371A ILE* 4.6 6.1 - - + -
444A ARG* 3.5 38.1 - - - +
447A TRP* 3.0 23.1 + - - +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO* 1.3 81.5 - - - +
304A LEU* 1.3 72.9 + - - +
305A TYR* 3.8 2.4 + - + +
329A ILE* 3.9 4.5 - - - -
330A PRO* 3.7 5.6 - - + +
332A THR* 3.9 17.3 - - + -
349A LEU* 4.1 15.0 - - + -
363A ALA* 3.6 19.3 - - + +
364A VAL* 4.2 13.7 - - + -
367A ALA* 3.5 24.9 - - + -
369A LEU 3.0 6.1 + - - +
370A ILE* 3.6 5.4 - - + -
371A ILE* 2.9 27.5 + - - +
447A TRP* 3.7 11.2 - - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 1.3 72.7 - - - +
305A TYR* 1.3 60.8 + - - +
306A VAL* 3.7 6.1 - - + -
320A LEU* 3.7 26.7 - - + -
323A LEU* 4.2 23.1 - - + -
324A SER* 4.5 5.2 - - - -
329A ILE* 3.8 23.1 - - + +
330A PRO 2.9 13.8 + - - +
331A VAL* 4.0 17.2 - - + +
332A THR* 2.9 32.6 + - - +
371A ILE* 3.4 32.1 - - + +
373A VAL* 3.5 22.0 - - + -
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 3.8 2.6 + - + -
304A LEU* 1.3 70.6 - - - +
306A VAL* 1.3 61.4 + - - +
332A THR* 3.5 9.9 - - + -
334A THR* 3.4 26.8 - - + +
352A LEU* 4.0 21.5 - - + -
364A VAL* 5.5 2.5 - - + -
370A ILE* 4.0 20.4 - - + -
371A ILE 3.0 8.8 + - - +
372A ALA* 3.2 18.7 - - + -
373A VAL 2.8 24.8 + - - +
375A ALA* 3.3 18.6 - - + +
376A ARG 4.0 0.5 + - - -
377A PHE* 2.9 62.3 + + - -
378A ASP* 4.3 0.9 + - - -
381A VAL* 3.6 24.5 - - + +
388A PHE* 5.3 4.7 - + - -
701A FAD 4.8 0.5 + - - -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.2 9.4 - - + -
305A TYR* 1.3 77.4 - - - +
307A GLY* 1.3 64.0 + - - +
310A ILE* 3.5 33.9 - - + -
320A LEU* 3.8 32.8 - - + -
331A VAL* 4.0 11.4 - - + -
332A THR 2.9 13.2 + - - +
333A THR* 3.0 15.0 - - + -
334A THR* 3.0 25.9 + - - +
340A SER* 3.8 11.7 - - - +
373A VAL* 3.5 16.4 - - + +
375A ALA* 4.4 2.7 - - - -
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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