Contacts of the strand formed by residues 467 - 472 (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 467 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B TRP* 3.4 21.5 - + + -
65B ASP 3.4 26.0 - - - -
66B HIS* 4.0 10.9 - - + -
81B ALA* 3.5 22.2 - - + -
82B GLU* 3.5 36.9 + - - +
461B PHE* 3.4 5.7 - - - +
462B SER* 2.9 26.9 + - - -
465B ALA 3.9 0.5 - - - -
466B LYS* 1.3 115.1 + - + +
468B TYR* 1.3 66.8 + - - +
482B LEU* 4.7 1.6 - - + -
483B HIS 3.2 17.7 - - - +
484B SER* 3.6 20.4 - - - -
485B SER* 4.3 1.1 - - - -
491B LEU* 3.9 17.7 - - + -
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Residues in contact with TYR 468 (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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62B TRP* 4.3 1.1 - - - -
416B TYR* 5.3 1.6 - + - -
431B LEU* 3.7 20.0 - - + -
445B LEU* 3.9 13.0 + - + +
459B VAL* 3.8 19.1 - - + -
460B SER 3.5 7.0 - - - -
461B PHE* 3.4 33.0 - + + -
467B TYR* 1.3 76.3 - - - +
469B GLN* 1.3 58.9 + - - +
470B LEU* 3.7 18.8 - - + -
482B LEU* 3.9 4.3 - - - -
483B HIS* 3.0 57.4 + + + +
484B SER 4.3 0.4 - - - -
485B SER* 3.5 26.9 - - - -
488B ASP* 2.9 40.0 + - - +
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Residues in contact with GLN 469 (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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58B TYR* 3.1 18.6 + - - -
60B LEU* 2.8 50.5 - - + +
62B TRP* 4.3 0.6 - - + -
459B VAL* 3.3 6.7 - - - +
460B SER* 3.0 39.3 + - - +
468B TYR* 1.3 72.9 - - - +
470B LEU* 1.3 70.5 + - - +
471B ARG* 3.0 29.9 + - + +
480B TYR* 3.3 21.8 - - - +
481B THR 3.2 13.0 - - - +
482B LEU* 4.1 7.1 - - + +
494B LEU* 3.9 4.2 - - + +
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Residues in contact with LEU 470 (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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431B LEU* 3.4 36.1 - - + -
445B LEU 4.4 3.6 - - - +
446B SER* 4.3 6.5 - - - -
449B LEU* 3.3 34.3 - - + -
457B TYR* 4.0 16.2 - - + -
458B SER 3.8 3.6 - - - +
459B VAL* 3.9 12.8 - - + -
468B TYR* 3.7 17.4 + - + -
469B GLN* 1.3 75.4 - - - +
471B ARG* 1.3 60.8 + - - +
472B CYS 4.0 0.7 - - - -
479B LEU 3.6 1.8 - - - +
480B TYR* 3.3 6.2 - - - -
481B THR* 2.8 40.7 + - - +
483B HIS* 3.4 18.2 - - + +
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Residues in contact with ARG 471 (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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57B LEU* 5.7 1.0 - - - +
58B TYR 3.1 20.2 + - - -
59B SER* 4.0 6.5 + - - +
60B LEU* 3.6 23.2 + - - +
456B TYR 3.6 0.3 - - - +
457B TYR* 3.1 8.6 - - - -
458B SER* 2.9 55.3 + - - +
459B VAL 5.2 1.1 - - - +
460B SER* 4.6 15.8 + - - +
469B GLN* 3.0 29.7 + - + +
470B LEU* 1.3 74.6 - - - +
472B CYS* 1.3 62.6 + - - +
473B SER* 3.9 4.9 + - - +
479B LEU 3.9 2.7 - - - -
480B TYR* 3.2 35.8 + - + -
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Residues in contact with CYS 472 (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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453B ARG 3.7 6.3 - - - -
454B CYS* 2.0 55.0 - - - -
456B TYR 3.5 5.4 - - - -
457B TYR* 3.8 15.7 - - + -
470B LEU 4.0 0.6 - - - -
471B ARG* 1.3 74.2 - - - +
473B SER* 1.3 61.0 + - - +
474B GLY 4.0 4.5 - - - -
477B LEU 4.5 5.2 - - - -
478B PRO* 3.3 9.2 - - - +
479B LEU* 2.9 43.4 + - + +
480B TYR* 5.2 1.7 - - - -
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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