Contacts of the strand formed by residues 344 - 350 (chain B) in PDB entry 4N41
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 THR 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B GLN* 2.8 18.9 + - - +
343B GLU* 1.3 78.1 + - - +
345B ALA* 1.3 62.9 + - - +
346B LEU* 3.6 25.8 - - + -
369B PHE* 3.5 23.6 - - + -
375B SER 3.0 7.1 + - - +
376B LEU* 3.3 7.7 - - - +
377B ARG* 2.9 24.8 + - - +
404B GLN* 3.2 15.4 + - - +
455B LEU* 5.5 0.2 - - + -
458B ALA* 4.3 1.6 - - + -
460B LEU* 3.3 31.2 - - + +
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Residues in contact with ALA 345 (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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344B THR* 1.3 73.8 - - - +
346B LEU* 1.3 69.4 + - - +
377B ARG* 3.1 44.1 - - + +
379B HIS* 3.8 9.9 - - + +
402B GLY 3.6 17.7 + - - +
403B VAL* 3.7 1.2 - - - -
404B GLN* 3.1 32.0 + - - +
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Residues in contact with LEU 346 (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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344B THR* 3.6 16.8 - - + -
345B ALA* 1.3 83.5 - - - +
347B ALA* 1.3 61.7 + - - +
357B TRP* 4.1 16.8 - - + -
365B LEU* 4.6 7.4 - - + -
369B PHE* 4.4 1.3 - - + -
376B LEU* 3.7 26.9 - - + -
377B ARG 2.9 7.6 + - - +
378B LEU* 3.5 6.9 - - + -
379B HIS* 2.9 24.7 + - - -
403B VAL* 4.5 1.8 - - - -
405B ALA* 3.5 14.8 - - + +
454B LEU* 4.1 24.9 - - + +
455B LEU* 4.1 22.2 - - + -
458B ALA* 3.9 19.5 - - + -
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Residues in contact with ALA 347 (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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346B LEU* 1.3 76.3 - - - +
348B LEU* 1.3 60.6 + - - +
357B TRP* 4.0 4.4 - - - -
379B HIS* 3.5 12.6 - - + -
381B LEU* 4.6 13.2 - - + -
398B ALA* 5.2 2.0 - - + -
403B VAL* 3.5 29.8 - - + -
405B ALA 2.9 9.9 + - - +
406B VAL* 3.4 13.9 - - + +
407B LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 348 (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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347B ALA* 1.3 73.8 - - - +
349B LEU* 1.3 67.0 + - - +
350B ARG* 3.8 23.7 + - + +
356B GLY* 3.4 37.2 - - - +
357B TRP* 3.4 37.9 - - + +
358B PRO* 4.7 1.1 - - + -
379B HIS 2.9 10.2 + - - +
380B THR* 3.6 9.5 - - + +
381B LEU* 2.8 32.9 + - - +
406B VAL* 4.5 0.2 - - - -
407B LEU* 3.6 23.3 - - + +
409B LEU* 4.2 19.3 - - + -
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Residues in contact with LEU 349 (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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347B ALA 4.1 0.4 + - - -
348B LEU* 1.3 73.6 - - - +
350B ARG* 1.3 64.7 + - - +
351B LEU* 3.8 23.1 - - + -
381B LEU* 4.0 20.9 - - + +
383B ALA 3.7 22.7 - - - +
391B PHE* 3.9 31.4 - - + -
406B VAL* 3.8 14.4 - - + -
407B LEU 2.9 10.2 + - - +
408B VAL* 3.3 22.1 - - + +
409B LEU 2.9 26.7 + - - +
421B LEU* 4.7 6.7 - - + -
425B LEU* 4.5 11.2 - - + -
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Residues in contact with ARG 350 (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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348B LEU* 3.8 21.0 + - + -
349B LEU* 1.3 79.3 - - - +
351B LEU* 1.3 69.0 + - - +
352B ASP* 2.3 48.0 + - - +
353B GLY 5.1 1.1 + - - -
354B ALA* 3.1 39.4 + - - +
355B GLN* 3.5 6.1 + - - +
356B GLY 2.9 42.9 + - - +
358B PRO* 4.7 5.3 - - - +
380B THR* 6.0 2.9 - - + -
381B LEU 5.1 3.4 + - - -
383B ALA 5.0 2.3 - - - +
384B HIS* 4.9 4.2 - - - -
409B LEU* 3.6 26.6 - - + +
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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