Contacts of the strand formed by residues 302 - 306 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ALA* 3.9 15.0 - - + -
300B LYS 3.3 11.4 - - - +
301B LYS* 1.3 89.0 - - - +
303B VAL* 1.3 62.5 + - - +
329B ILE* 3.9 24.5 - - + -
330B PRO* 3.2 11.6 - - - +
368B ASP* 3.5 1.7 - - - +
369B LEU* 3.5 9.9 - - + +
371B ILE* 4.7 6.1 - - + -
444B ARG* 3.4 38.4 - - - +
447B TRP* 2.8 29.5 + - + -
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PRO* 1.3 82.0 - - - +
304B LEU* 1.3 72.5 + - - +
305B TYR* 3.6 3.4 + - + +
329B ILE* 4.0 2.9 - - - -
330B PRO* 3.8 7.6 - - + -
332B THR* 4.0 15.9 - - + -
349B LEU* 4.2 10.3 - - + -
363B ALA* 3.6 18.6 - - + +
364B VAL* 4.3 13.5 - - + -
367B ALA* 3.4 27.1 - - + -
369B LEU 3.0 7.5 + - - +
370B ILE* 3.5 8.4 - - + +
371B ILE* 2.9 28.1 + - - +
447B TRP* 3.8 10.1 - - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 1.3 72.1 - - - +
305B TYR* 1.3 60.1 + - - +
306B VAL* 3.7 2.4 + - + -
320B LEU* 3.9 17.9 - - + -
323B LEU* 4.3 21.5 - - + -
324B SER* 4.3 10.5 - - - -
329B ILE* 3.7 22.2 - - + +
330B PRO 2.9 9.6 + - - +
331B VAL* 3.5 34.0 - - + +
332B THR* 2.8 33.3 + - - +
371B ILE* 3.6 36.1 - - + +
373B VAL* 3.8 17.3 - - + -
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 3.6 2.8 + - + -
304B LEU* 1.3 69.2 - - - +
306B VAL* 1.3 61.0 + - - +
332B THR* 3.6 9.4 - - + -
334B THR* 3.4 27.4 - - + +
352B LEU* 4.0 20.2 - - + -
364B VAL* 5.9 2.2 - - + -
370B ILE* 3.8 21.1 - - + -
371B ILE 3.1 9.3 + - - +
372B ALA* 3.3 16.1 - - + -
373B VAL 2.8 24.3 + - - +
375B ALA* 3.3 20.6 - - + +
376B ARG 4.2 0.3 + - - -
377B PHE* 3.2 58.2 + + - -
378B ASP* 4.5 1.2 + - - -
381B VAL* 3.7 25.5 - - + +
388B PHE* 5.6 4.3 - + - -
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 4.2 7.9 - - + +
305B TYR* 1.3 75.3 - - - +
307B GLY* 1.3 62.7 + - - +
310B ILE* 3.5 35.9 - - + -
320B LEU* 3.6 24.7 - - + -
331B VAL* 3.6 25.8 - - + -
332B THR 2.9 9.5 + - - +
333B THR* 3.2 12.3 - - + -
334B THR* 3.0 28.1 + - - +
340B SER* 3.9 9.4 - - - +
373B VAL* 3.5 14.4 - - + +
375B ALA* 4.5 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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