Contacts of the strand formed by residues 404 - 410 (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 VAL 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B ARG* 3.0 20.3 + - - -
374B ILE* 3.6 23.1 - - + +
382B ARG 3.0 15.4 + - - +
383B HIS* 4.2 2.2 - - - +
384B ILE* 3.8 32.8 - - + -
398B THR* 3.9 14.8 - - + +
402B TRP* 3.9 16.8 - - + -
403B GLU* 1.3 72.3 - - - +
405B ILE* 1.3 63.2 + - - +
406B GLY 3.6 17.5 - - - +
417B TYR* 3.9 13.5 - - + -
418B ILE 3.6 12.3 - - - +
419B SER* 4.0 0.9 - - - -
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Residues in contact with ILE 405 (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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356B ARG* 3.1 19.2 + - - +
374B ILE* 4.0 2.5 - - - +
403B GLU 4.1 8.1 - - - +
404B VAL* 1.3 76.1 - - - +
406B GLY* 1.3 59.3 + - - +
418B ILE* 2.8 35.2 + - + +
419B SER* 4.1 7.6 - - - -
420B ASN* 4.6 8.1 - - + +
429B ARG* 3.9 35.4 - - - +
585B TYR* 3.3 44.6 - - + +
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Residues in contact with GLY 406 (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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374B ILE* 3.5 10.8 - - - -
404B VAL* 3.4 4.5 - - - +
405B ILE* 1.3 82.9 - - - +
407B ILE* 1.3 66.0 + - - -
408B GLU* 3.7 11.0 - - - +
417B TYR* 3.6 3.8 - - - +
418B ILE* 3.2 25.2 + - - +
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Residues in contact with ILE 407 (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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361B GLU 5.1 0.4 - - - +
363B HIS* 3.6 58.1 + - + +
372B TYR* 4.1 15.3 - - + +
373B LYS* 4.4 1.1 - - - -
374B ILE* 3.9 20.0 - - + +
384B ILE* 3.7 46.7 - - + -
406B GLY* 1.3 72.5 - - - -
408B GLU* 1.3 66.5 + - - +
409B ALA 4.3 9.0 - - - +
410B LEU* 5.6 1.6 - - + -
415B LEU* 4.1 15.3 - - + -
416B TYR 3.9 11.0 - - - +
417B TYR* 4.4 0.4 - - - -
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Residues in contact with GLU 408 (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 HIS* 5.7 2.1 - - - -
406B GLY* 3.7 15.8 - - - +
407B ILE* 1.3 83.5 - - - +
409B ALA* 1.3 63.6 + - - +
416B TYR* 3.0 12.4 + - + +
417B TYR* 4.5 1.3 - - - -
418B ILE* 4.1 25.0 - - + +
431B LEU* 5.0 0.4 - - + -
459B VAL* 3.5 41.1 + - + +
461B PHE* 4.0 14.1 - - + +
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Residues in contact with ALA 409 (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 HIS* 6.3 0.2 - - - -
407B ILE* 3.9 4.7 - - - +
408B GLU* 1.3 81.0 - - - +
410B LEU* 1.3 62.8 + - - +
415B LEU* 3.4 6.1 - - - +
416B TYR* 2.8 49.9 + - + +
461B PHE* 3.8 27.4 - - + -
465B ALA* 4.5 8.7 - - + -
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Residues in contact with LEU 410 (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 HIS* 4.4 11.9 - - + +
364B PHE 3.3 32.1 - - - +
365B THR* 3.9 13.2 - - + -
366B LEU* 5.5 6.1 - - + +
372B TYR* 3.9 30.1 - - + -
407B ILE* 5.6 1.3 - - + -
409B ALA* 1.3 77.4 - - - +
411B THR* 1.3 90.3 + - - +
414B TYR 3.4 9.2 - - - +
415B LEU* 4.2 11.0 - - + -
436B LEU* 3.9 12.3 - - + -
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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