Contacts of the strand formed by residues 378 - 383 (chain B) in PDB entry 3NUI
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 MET 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TRP* 4.1 17.7 - - + -
225B VAL* 3.7 30.3 - - + +
227B GLY* 4.8 4.5 - - - -
231B VAL* 3.6 12.7 - - + +
259B ILE* 3.7 24.9 - - + -
260B CYS* 4.1 4.5 - - - -
264B ARG* 4.0 22.4 - - + +
265B THR* 3.8 27.1 - - - -
374B GLY* 3.0 22.7 - - - -
375B ILE* 3.0 31.2 + - + +
377B PHE* 1.3 79.4 - - - +
379B TRP* 1.3 61.8 + - - +
423B LEU 3.5 3.8 - - - -
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Residues in contact with TRP 379 (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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231B VAL* 3.7 6.5 - - - +
353B ALA* 4.1 9.4 - - + -
356B PHE* 3.5 35.9 - + + -
357B GLU* 3.5 34.8 - - + -
360B LEU* 3.4 31.4 - - + -
372B TYR* 3.8 23.6 - + - -
373B ARG 3.2 9.2 - - - -
374B GLY* 3.4 37.9 - - - -
375B ILE* 3.6 19.1 - - - -
376B GLY 2.7 27.2 + - - -
378B MET* 1.3 90.6 - - - +
380B ALA* 1.3 62.0 + - - +
422B VAL* 3.4 6.8 - - - +
423B LEU* 2.8 37.9 + - + +
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Residues in contact with ALA 380 (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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230B GLY 3.4 25.8 - - - +
231B VAL* 4.1 2.5 - - + -
360B LEU* 5.4 0.8 - - - +
371B GLU 4.0 0.2 - - - +
372B TYR* 3.3 6.8 - - - +
373B ARG* 2.7 53.8 + - + +
379B TRP* 1.3 76.6 - - - +
381B LEU* 1.3 66.3 + - - +
420B SER* 4.6 1.6 - - - -
421B VAL 3.3 12.1 - - - +
422B VAL* 4.0 8.3 - - + -
423B LEU* 6.4 0.4 - - - -
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Residues in contact with LEU 381 (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 LEU* 4.1 25.4 - - + +
363B ILE* 4.1 23.6 - - + -
369B ILE* 4.0 28.0 - - + -
371B GLU 3.7 0.4 - - - -
372B TYR* 3.7 27.6 - - + -
380B ALA* 1.3 75.4 - - - +
382B GLU* 1.3 62.8 + - - +
383B ALA 4.0 0.7 + - - -
420B SER* 3.1 5.8 - - - -
421B VAL* 2.9 42.1 + - + +
423B LEU* 4.8 5.8 - - + -
441B LEU* 3.6 31.0 - - + -
445B LEU* 5.0 4.7 - - + -
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Residues in contact with GLU 382 (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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183B HIS* 4.3 1.6 - - - -
185B TRP* 3.9 19.1 - - + -
186B ARG* 2.8 31.9 + - - -
369B ILE* 3.4 5.9 - - - +
370B GLY 2.7 32.7 + - - -
371B GLU* 3.0 22.1 + - + +
373B ARG* 2.8 37.7 + - - +
381B LEU* 1.3 74.4 - - - +
383B ALA* 1.3 65.5 + - - +
384B VAL* 5.6 0.3 - - - +
419B GLN* 3.9 17.7 + - - +
420B SER* 3.2 16.3 + - - +
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Residues in contact with ALA 383 (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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368B ASN 3.2 10.3 - - - +
369B ILE* 4.7 3.3 - - + +
381B LEU 4.0 1.4 + - - -
382B GLU* 1.3 77.0 - - - +
384B VAL* 1.3 66.7 + - - +
392B PRO* 4.5 5.9 - - - +
393B PHE* 4.5 6.7 - - + -
399B VAL* 4.3 17.0 - - + -
400B SER* 5.5 1.3 - - - +
403B ILE* 4.7 8.1 - - + -
419B GLN* 2.9 30.1 + - + +
449B PHE* 4.3 20.2 - - + -
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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