Contacts of the strand formed by residues 411 - 419 (chain B) in PDB entry 1SOX
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 ALA 411 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370B TYR* 3.6 1.0 - - - -
371B ALA* 2.8 37.5 + - + +
379B VAL* 4.2 27.9 - - + +
397B LEU* 4.9 12.8 - - + -
398B MET 4.3 12.8 - - - +
409B ALA 5.3 0.4 - - - +
410B TRP* 1.3 74.3 - - - +
412B LEU* 1.3 64.4 + - - +
413B TRP* 3.7 1.6 + - - -
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Residues in contact with LEU 412 (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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125B ALA* 3.4 42.0 - - + +
127B ARG* 3.8 6.3 - - - +
128B PHE* 3.8 34.5 - - + +
369B GLY 3.6 3.8 - - - +
370B TYR* 4.0 10.1 - - + -
397B LEU* 3.8 0.9 - - - -
398B MET* 2.7 49.1 + - + +
399B GLY* 5.8 0.2 - - - -
410B TRP* 3.7 36.9 + - + +
411B ALA* 1.3 73.5 - - - +
413B TRP* 1.3 55.8 + - - +
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Residues in contact with TRP 413 (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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125B ALA* 5.7 0.2 - - - +
349B SER* 4.8 0.2 - - - -
350B ALA 3.5 9.6 + - - -
351B VAL* 4.1 5.8 - - + -
367B VAL* 3.7 34.8 - - + -
368B LYS* 3.3 15.4 - - - +
369B GLY* 3.0 47.0 + - - +
370B TYR 3.1 31.6 + - - +
371B ALA* 4.0 2.8 - - + +
382B VAL* 3.9 25.8 - - + +
384B VAL* 3.6 22.0 - - + -
395B ALA* 3.8 15.7 - - + -
396B ARG 3.2 12.3 - - - +
397B LEU* 4.0 15.7 - - + -
398B MET* 4.4 2.7 - - - -
411B ALA 4.1 0.7 - - - -
412B LEU* 1.3 75.1 - - - +
414B GLU* 1.3 71.6 + - - +
415B LEU 4.7 1.1 - - - -
429B CYS* 3.8 23.5 - - + -
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Residues in contact with GLU 414 (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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366B THR* 3.4 20.2 - - + +
367B VAL 3.1 11.7 - - - +
368B LYS* 4.2 18.9 - - + -
396B ARG* 2.9 75.6 + - - +
398B MET* 3.6 21.0 - - + +
413B TRP* 1.3 81.7 - - - +
415B LEU* 1.3 61.2 + - - +
416B THR* 4.2 3.6 + - - -
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Residues in contact with LEU 415 (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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365B LEU 3.6 1.2 - - - +
366B THR* 3.6 1.1 - - - -
367B VAL* 2.8 40.2 + - + +
384B VAL* 3.7 36.8 - - + +
386B LEU* 5.8 2.7 - - + -
393B LYS* 3.8 34.3 - - + +
394B VAL 3.7 19.7 - - - +
395B ALA* 4.2 9.6 - - + -
396B ARG* 5.1 2.9 - - - +
413B TRP* 5.0 0.4 - - + -
414B GLU* 1.3 78.3 - - - +
416B THR* 1.3 74.0 + - - +
417B VAL* 3.9 8.1 + - + +
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Residues in contact with THR 416 (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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364B GLU* 3.7 38.5 - - + +
365B LEU 3.3 10.3 - - - +
366B THR* 3.0 25.3 + - - +
393B LYS* 6.1 0.2 - - - +
396B ARG* 4.6 9.4 + - - +
414B GLU* 4.2 5.9 + - - -
415B LEU* 1.3 81.2 - - - +
417B VAL* 1.3 64.1 + - - +
418B PRO* 4.7 0.3 - - - +
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Residues in contact with VAL 417 (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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364B GLU* 3.5 4.9 - - - -
365B LEU* 2.8 41.1 + - + +
367B VAL* 4.6 8.1 - - + -
386B LEU* 3.3 45.1 - - + -
393B LYS* 4.0 25.6 - - + -
415B LEU* 4.8 8.7 - - + +
416B THR* 1.3 76.4 - - - +
418B PRO* 1.3 78.5 - - + +
419B VAL* 3.7 10.2 + - + -
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Residues in contact with PRO 418 (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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363B GLY 3.2 11.0 - - - +
364B GLU* 4.3 13.4 - - + +
386B LEU* 4.8 2.9 - - - +
393B LYS* 5.9 0.4 - - - -
416B THR 4.7 0.7 - - - +
417B VAL* 1.3 103.0 - - + +
419B VAL* 1.3 63.1 + - - +
420B GLU* 4.4 1.5 + - - +
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Residues in contact with VAL 419 (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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360B VAL* 4.7 2.2 - - + -
361B PRO 3.6 24.0 - - - +
362B PRO* 3.9 0.2 - - - +
363B GLY* 2.5 49.1 + - - +
365B LEU* 4.0 30.5 - - + -
386B LEU* 5.0 2.5 - - + -
417B VAL* 4.3 7.6 - - + +
418B PRO* 1.3 79.2 - - - +
420B GLU* 1.3 62.4 + - - +
421B ALA 4.0 0.2 + - - -
425B LEU* 3.7 32.5 - - + -
464B VAL* 3.9 16.8 - - + -
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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