Contacts of the strand formed by residues 331 - 339 (chain B) in PDB entry 1XDS
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 LEU 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B LEU* 3.9 15.3 - - + -
274B VAL* 3.4 34.1 - - + -
277B LEU* 4.1 15.0 - - + -
283B LEU* 3.6 27.6 - - + -
323B VAL 4.7 1.2 - - - +
326B ALA* 3.0 26.1 + - + +
327B GLY* 3.4 22.6 + - - -
329B ALA* 4.4 3.1 - - + -
330B GLY* 1.3 77.6 - - - +
332B ALA* 1.3 60.4 + - - +
353B PHE* 4.1 16.3 - - + -
354B THR 3.4 22.7 - - - +
355B ALA* 4.1 4.3 - - - +
356B VAL* 3.6 5.3 - - - +
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Residues in contact with ALA 332 (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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331B LEU* 1.3 75.2 - - - +
333B LEU* 1.3 67.9 + - - +
353B PHE* 3.3 6.2 - - - -
354B THR* 3.1 39.2 + - - +
355B ALA 5.8 0.2 - - - +
356B VAL* 3.9 13.4 - - + +
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Residues in contact with LEU 333 (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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319B ARG* 4.4 16.2 - - - +
323B VAL* 4.3 26.8 - - + +
332B ALA* 1.3 76.0 - - - +
334B ALA* 1.3 59.3 + - - +
335B SER* 3.4 29.8 - - - +
336B GLU* 5.0 6.5 - - + -
351B LEU* 4.1 17.9 - - + -
352B GLU 3.5 9.4 - - - +
353B PHE* 3.6 25.8 - - + -
354B THR* 5.6 0.2 - - - -
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Residues in contact with ALA 334 (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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282B ARG* 6.2 1.8 - - - +
332B ALA 3.5 1.3 + - - +
333B LEU* 1.3 75.2 - - - +
335B SER* 1.3 63.8 + - - +
352B GLU* 3.0 28.6 + - + +
354B THR* 4.3 23.3 - - + +
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Residues in contact with SER 335 (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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333B LEU* 3.4 15.4 - - - +
334B ALA* 1.3 81.0 - - - +
336B GLU* 1.3 61.4 + - - +
337B ARG* 3.1 23.6 + - - -
350B ILE 4.6 0.4 - - - -
351B LEU* 3.7 1.2 - - - -
352B GLU* 2.7 56.9 + - - +
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Residues in contact with GLU 336 (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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291B VAL* 3.4 28.7 - - - +
319B ARG* 3.6 23.1 + - - +
333B LEU* 5.0 7.6 - - + -
335B SER* 1.3 76.7 - - - +
337B ARG* 1.3 73.2 + - - +
338B THR* 5.2 3.8 + - - -
349B SER* 4.6 6.9 + - - -
350B ILE 3.7 3.6 - - - -
351B LEU* 3.3 25.3 - - + +
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Residues in contact with ARG 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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177B ALA* 3.1 39.1 + - + -
178B TYR* 3.3 27.3 - - - +
179B ASP 5.1 1.0 - - - +
335B SER* 3.1 31.7 + - - -
336B GLU* 1.3 80.9 + - - +
338B THR* 1.3 65.9 + - - +
349B SER* 3.3 9.9 + - - -
350B ILE* 3.0 57.1 + - + +
352B GLU* 4.1 8.1 + - - +
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Residues in contact with THR 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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294B ASP* 5.6 2.7 + - - +
336B GLU* 5.2 4.2 + - - -
337B ARG* 1.3 81.3 + - - +
339B SER* 1.3 80.6 + - - +
347B ASP* 4.4 18.2 - - + +
348B PHE 3.5 10.1 + - - +
349B SER* 4.4 6.7 + - - +
350B ILE* 5.6 3.2 - - - +
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Residues in contact with SER 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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173B ALA* 3.6 23.7 + - - +
177B ALA* 5.5 1.9 - - - +
338B THR* 1.3 90.6 + - - +
340B GLY* 1.3 59.7 + - - +
347B ASP* 3.5 3.7 - - - +
348B PHE* 3.1 51.7 + - - -
350B ILE* 5.2 3.1 - - - +
9600B DRA 5.5 0.8 - - - +
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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