Contacts of the strand formed by residues 336 - 341 (chain B) in PDB entry 4TR8
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 GLN 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B VAL* 3.8 21.8 - - + +
259B GLY 3.2 15.8 + - - +
260B ASP* 5.0 3.3 - - + +
261B ARG* 4.5 0.4 - - - -
310B GLU* 2.9 29.5 + - - +
332B ILE* 4.0 0.7 - - - +
334B THR* 2.7 31.9 + - - +
335B GLU* 1.3 90.9 - - + +
337B VAL* 1.3 61.1 + - - +
353B ALA* 3.4 22.7 + - + +
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Residues in contact with VAL 337 (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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257B VAL 3.6 1.2 - - - +
258B VAL* 3.5 5.4 - - - +
259B GLY 2.8 39.7 + - - +
261B ARG* 4.0 9.0 - - + -
264B LEU* 3.6 25.4 - - + -
329B LEU* 3.9 22.2 - - + -
332B ILE* 4.0 15.9 - - + -
336B GLN* 1.3 73.7 - - - +
338B ARG* 1.3 66.6 + - - +
339B PHE* 3.8 11.5 + - + -
350B VAL* 3.4 29.6 - - + -
351B HIS 3.6 7.4 - - - +
353B ALA 4.7 0.4 - - - +
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Residues in contact with ARG 338 (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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256B LEU* 4.0 21.3 - - + +
257B VAL 3.4 2.9 - - - -
258B VAL* 4.1 20.6 - - + -
337B VAL* 1.3 75.7 - - - +
339B PHE* 1.3 62.3 + - - +
340B ILE* 4.5 10.8 - - + +
349B LEU 3.8 0.2 - - - +
350B VAL* 3.2 9.0 - - - +
351B HIS* 2.9 56.1 + - + +
352B GLU 3.0 17.5 + - - +
353B ALA* 3.2 19.0 + - - +
354B ASP 4.7 1.0 - - - -
355B ASN 3.0 27.5 + - - +
356B ASP* 2.7 31.3 + - - -
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Residues in contact with PHE 339 (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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255B LYS 3.5 2.3 - - - +
256B LEU* 3.6 2.1 - - - +
257B VAL* 2.9 51.5 + - + +
259B GLY 6.0 0.2 - - - -
264B LEU* 4.3 12.6 - - + -
268B PHE* 4.5 19.1 - + - -
284B LEU* 5.8 6.7 - - + -
320B PHE* 6.2 1.8 - + - -
325B LEU* 4.3 21.3 - - + -
328B VAL* 5.6 1.8 - - + -
329B LEU* 4.1 17.3 - - + -
337B VAL* 3.8 33.2 - - + -
338B ARG* 1.3 77.7 - - - +
340B ILE* 1.3 62.5 + - - +
341B LEU* 4.0 15.0 - - + -
348B ALA* 4.5 12.6 - - + -
349B LEU 3.5 3.1 - - - -
350B VAL* 3.6 26.5 - - + -
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Residues in contact with ILE 340 (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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250B PRO* 5.6 0.2 - - - +
253B GLY* 3.7 30.0 - - - +
255B LYS 3.3 8.7 - - - +
256B LEU* 4.0 19.1 - - + -
338B ARG* 4.5 13.0 - - + +
339B PHE* 1.3 76.2 - - - +
341B LEU* 1.3 60.7 + - - +
347B SER 4.2 1.9 - - - +
348B ALA* 3.8 2.9 - - - -
349B LEU* 2.7 57.1 + - + +
351B HIS* 3.7 32.5 - - + +
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Residues in contact with LEU 341 (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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253B GLY* 3.5 3.1 - - - -
254B ASP* 3.0 8.0 + - - -
255B LYS* 2.9 37.0 + - + +
257B VAL* 4.3 12.1 - - + -
284B LEU* 5.8 6.1 - - + -
286B LEU* 4.2 17.9 - - + -
291B LEU* 6.3 2.5 - - + -
316B LEU* 3.9 26.0 - - + -
318B ILE* 4.7 12.8 - - + -
320B PHE* 4.6 11.9 - - + -
339B PHE* 4.5 15.0 - - + -
340B ILE* 1.3 78.6 - - - +
342B SER* 1.3 61.8 + - - +
347B SER 4.7 4.0 - - - +
348B ALA* 3.5 34.1 - - + -
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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