Contacts of the strand formed by residues 410 - 414 (chain B) in PDB entry 1IAX
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 TRP 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B SER* 3.5 21.3 - - - -
178B PHE* 3.8 13.4 - + - -
357B CYS 5.3 0.7 - - - -
358B LEU* 4.0 19.5 - - + -
367B TRP* 3.2 68.6 - + + -
368B MET 3.1 18.2 - - - -
369B ASP* 3.4 34.8 - - + -
371B ARG* 3.7 13.8 - - - +
382B GLU* 4.4 1.4 + - - +
400B GLY* 2.6 35.4 + - - -
405B CYS* 4.3 4.3 - - - -
407B GLU* 3.2 43.8 + - + -
408B PRO 3.5 3.3 - - - -
409B GLY* 1.3 79.2 - - - +
411B PHE* 1.3 57.9 + - - +
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TRP* 4.1 3.4 - - - -
368B MET* 2.8 49.9 + - + +
370B LEU* 3.7 15.5 - - + -
382B GLU* 3.8 23.1 - - + -
385B LEU* 3.5 36.3 - - + -
386B TRP* 3.5 36.3 - + + -
389B ILE* 4.4 3.4 - - + -
397B VAL* 3.9 15.5 - - + -
398B SER 3.1 7.0 - - - +
399B PRO* 3.6 20.4 - - + -
400B GLY 4.2 0.2 - - - +
409B GLY* 3.5 23.3 - - - -
410B TRP* 1.3 76.1 - - - +
412B ARG* 1.3 62.5 + - - +
413B VAL* 3.8 0.6 - - + +
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Residues in contact with ARG 412 (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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51B MET 4.2 2.6 - - - +
52B GLY* 2.7 30.5 + - - -
54B ALA* 3.6 12.5 - - - +
209B ASN* 3.0 23.7 + - - +
210B PRO* 3.6 22.7 - - + +
365B PHE* 3.9 22.2 - - + -
366B CYS 3.8 5.4 - - - +
367B TRP* 3.8 15.3 - - + -
397B VAL* 3.7 2.6 - - - +
398B SER* 2.7 37.5 + - - +
403B PHE* 3.7 29.7 - - + -
411B PHE* 1.3 72.2 - - - +
413B VAL* 1.3 64.7 + - - +
414B CYS* 3.7 11.6 - - - -
601B SO4 2.9 40.7 + - - -
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B MET* 3.5 41.5 - - + -
346B PHE* 3.9 20.6 - - + -
365B PHE* 3.3 4.6 - - - -
366B CYS* 3.0 35.9 + - - +
368B MET* 3.8 34.8 - - + -
397B VAL* 4.1 11.9 - - + -
411B PHE 3.8 11.4 - - - +
412B ARG* 1.3 79.3 - - - +
414B CYS* 1.3 62.0 + - - +
415B PHE* 4.0 1.6 + - - -
430B ILE* 5.7 2.7 - - + -
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Residues in contact with CYS 414 (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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51B MET* 2.9 50.9 + - - +
52B GLY 3.9 0.7 - - - -
53B LEU 3.2 38.6 - - - +
54B ALA* 3.5 11.2 - - - -
55B GLU 5.3 0.4 - - - +
364B LEU 3.7 8.5 - - - +
365B PHE* 4.0 8.3 - - - -
412B ARG* 3.7 24.9 - - - -
413B VAL* 1.3 73.5 - - - +
415B PHE* 1.3 60.4 + - - +
416B ALA 3.8 1.3 - - - +
417B ASN* 4.0 6.1 - - - +
418B MET* 4.0 3.8 - - - +
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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