Contacts of the strand formed by residues 414 - 419 (chain B) in PDB entry 1N1M
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 TYR 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409B ALA 4.4 0.2 - - - +
410B LEU* 3.4 2.1 - - - +
411B THR* 2.9 35.9 + - - +
413B ASP* 1.3 100.5 - - + +
415B LEU* 1.3 61.4 + - - +
416B TYR* 4.2 22.8 - - + -
433B LYS* 3.6 50.7 + - + -
434B ILE 3.3 25.6 - - - +
435B GLN* 3.5 32.1 + - + -
436B LEU* 3.6 5.8 - - - -
441B LYS* 5.2 1.3 - - + -
443B THR* 5.4 2.9 - - - -
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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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372B TYR* 3.4 51.8 - - + -
384B ILE* 3.8 30.1 - - + -
397B ILE* 4.4 3.1 - - + -
407B ILE* 4.1 12.3 - - + -
409B ALA 3.4 9.9 - - - +
410B LEU* 4.2 7.9 - - + -
414B TYR* 1.3 75.8 - - - +
416B TYR* 1.3 78.5 + - - +
417B TYR* 4.0 5.3 + - + -
433B LYS* 3.4 1.3 - - - -
434B ILE* 2.9 35.1 + - + +
436B LEU* 3.7 13.7 - - + -
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Residues in contact with TYR 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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407B ILE 3.9 0.3 - - - -
408B GLU* 3.0 22.1 + - - -
409B ALA* 2.8 32.8 + - + +
411B THR* 4.3 22.6 + - + +
414B TYR* 4.2 20.1 - - + +
415B LEU* 1.3 79.3 - - - +
417B TYR* 1.3 64.9 + - - +
431B LEU* 4.2 5.2 - - + -
432B TYR 3.2 8.1 - - - +
433B LYS* 3.4 39.5 + - + +
445B LEU* 4.3 9.2 - - + -
461B PHE* 3.4 42.4 - + + -
465B ALA* 4.7 2.4 + - + -
468B TYR* 5.3 1.3 - + - -
485B SER* 4.0 22.8 + - - -
488B ASP* 4.7 7.4 - - - -
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Residues in contact with TYR 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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384B ILE* 3.8 26.5 - - + -
398B THR* 4.1 17.8 - - + +
402B TRP* 3.8 15.0 - + - -
404B VAL* 3.9 16.2 - - + -
406B GLY 3.6 14.1 - - - +
407B ILE* 4.4 1.3 - - - -
408B GLU* 4.2 3.1 - - - +
415B LEU* 4.1 10.8 - - + -
416B TYR* 1.3 75.4 - - - +
418B ILE* 1.3 71.7 + - - +
419B SER* 3.6 22.2 - - - -
421B GLU* 4.1 2.3 + - - -
431B LEU* 3.5 5.0 - - - +
432B TYR* 2.7 68.0 + - + +
433B LYS 4.6 0.2 - - - -
434B ILE* 4.4 16.2 - - + -
442B VAL* 3.6 21.1 - - + +
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Residues in contact with ILE 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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404B VAL* 3.6 7.4 - - - +
405B ILE* 2.8 34.0 + - + -
406B GLY 3.2 9.9 + - - +
408B GLU* 4.1 18.8 - - + +
417B TYR* 1.3 76.7 - - - +
419B SER* 1.3 67.5 + - - +
429B ARG* 3.2 33.9 - - + -
430B ASN 3.0 14.1 - - - +
431B LEU* 4.3 9.0 - - + -
457B TYR* 3.5 22.2 - - + +
458B SER* 3.8 16.6 - - - -
459B VAL* 4.2 12.3 - - + +
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Residues in contact with SER 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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402B TRP* 3.5 19.6 - - - -
403B GLU 3.3 17.7 - - - -
404B VAL* 4.0 0.9 - - - -
405B ILE* 4.1 7.9 - - - -
417B TYR* 3.6 7.8 - - - -
418B ILE* 1.3 77.5 - - - +
420B ASN* 1.3 60.2 + - - +
421B GLU* 3.3 12.5 + - - +
422B TYR 5.2 0.2 + - - -
428B GLY 4.5 0.7 - - - -
429B ARG* 3.6 1.6 - - - -
430B ASN* 2.8 34.0 + - - +
432B TYR* 3.1 23.6 - - - -
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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