Contacts of the strand formed by residues 326 - 331 (chain B) in PDB entry 3IH9
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 ARG 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B ARG* 3.8 3.0 - - - -
323B GLU* 3.2 32.2 + - + +
324B GLY 3.6 0.7 + - - +
325B ASP* 1.3 93.5 - - + +
327B VAL* 1.3 64.3 + - - +
328B PHE* 3.8 29.3 - - + -
406B THR* 3.2 26.1 - - - +
408B VAL* 3.7 18.5 - - + +
438B ARG* 5.5 1.2 - - - +
440B GLU* 3.5 25.7 + - - -
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B VAL* 3.6 26.7 - - + -
321B GLU 3.2 11.9 - - - +
322B ARG* 3.3 26.7 - - - -
326B ARG* 1.3 74.5 - - - +
328B PHE* 1.3 68.2 + - - +
329B LEU* 3.9 4.2 + - + +
350B LEU* 4.6 10.3 - - + -
394B ALA* 4.5 5.8 - - + -
404B ILE* 3.5 31.2 - - + -
406B THR 3.0 6.3 + - - -
407B VAL* 3.4 14.8 - - + +
408B VAL* 2.9 28.2 + - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PHE* 3.5 3.5 - - - +
320B VAL* 3.4 5.2 - - - -
321B GLU* 2.6 61.4 + - + +
323B GLU* 3.5 33.0 - - + -
326B ARG* 3.8 37.0 - - + -
327B VAL* 1.3 76.5 - - - +
329B LEU* 1.3 59.2 + - - +
330B HIS* 3.9 23.5 + + + +
408B VAL* 3.9 26.9 - - + -
442B GLU* 5.7 3.4 - - - -
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Residues in contact with LEU 329 (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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317B VAL* 3.9 14.8 - - + -
319B PHE 3.8 0.7 - - - -
320B VAL* 3.2 36.1 - - + -
327B VAL* 3.9 4.6 + - + -
328B PHE* 1.3 71.2 - - - +
330B HIS* 1.3 62.0 + - - +
331B LEU* 4.1 13.9 - - + -
343B VAL* 4.3 11.0 - - + -
346B ALA* 4.5 12.1 - - + -
347B LEU* 3.8 29.2 - - + -
350B LEU* 6.1 4.9 - - + -
391B ALA* 5.2 1.6 - - + -
407B VAL* 4.8 9.2 - - + -
408B VAL 3.0 14.1 + - - +
409B LEU* 3.4 25.7 - - + +
410B ASN 3.1 22.5 + - - -
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Residues in contact with HIS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B VAL* 3.5 2.8 - - - +
318B ARG* 2.7 37.4 + - + -
319B PHE* 3.2 58.7 + + + +
321B GLU* 5.3 1.1 - - - -
328B PHE* 4.1 25.5 - + + -
329B LEU* 1.3 78.5 - - - +
331B LEU* 1.3 63.3 + - - +
408B VAL* 5.7 0.9 - - + -
410B ASN* 3.3 45.2 + - + +
413B ARG* 5.9 4.3 - - + -
442B GLU* 5.2 2.0 - - - -
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA 3.0 14.6 - - - +
317B VAL* 4.3 5.2 - - + -
318B ARG* 4.4 2.9 - - - +
329B LEU* 4.1 21.3 - - + -
330B HIS* 1.3 86.0 - - - +
332B GLN* 1.3 65.9 + - - +
335B ILE* 3.9 18.8 - - + -
343B VAL* 3.9 26.7 - - + -
409B LEU* 3.7 18.2 - - + -
410B ASN* 3.1 9.5 + - - +
411B LEU* 3.6 20.9 - - + -
413B ARG* 3.5 14.4 + - - +
414B VAL* 3.4 21.6 + - + +
417B ILE* 6.1 0.2 - - + -
425B ILE* 4.4 11.7 - - + -
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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
------------------------------------------------------------
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