Contacts of the strand formed by residues 349 - 352 (chain D) in PDB entry 2IB8
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 MET 349 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D ILE* 3.4 1.6 - - - +
348D ALA* 1.3 78.8 - - - +
350D TRP* 1.3 68.0 + - - +
351D GLU* 5.4 2.7 - - - +
373D LYS 3.6 3.8 - - - +
376D ILE* 4.1 28.3 - - + -
377D ASN* 5.8 0.9 - - - -
397D HIS* 5.4 5.6 - - - -
398D LEU* 3.7 21.1 - - + +
401D ALA* 3.5 49.8 - - + +
402D LEU* 3.7 21.8 - - + +
403D LYS* 6.3 0.2 - - + -
406D GLU* 4.4 7.0 - - - +
407D TYR 3.4 2.0 + - - -
408D GLY* 3.2 4.5 - - - -
409D LEU 3.1 23.0 + - - -
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Residues in contact with TRP 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D ALA* 4.2 11.7 - - + -
337D LEU* 4.3 14.1 - - + -
344D LYS* 3.8 20.5 + - + -
347D ILE* 3.4 32.8 + - + +
349D MET* 1.3 75.5 - - - +
351D GLU* 1.3 64.9 + - - +
352D VAL* 3.9 16.8 - - + -
367D LEU* 4.3 17.3 - - + -
369D ILE* 3.7 36.7 - - + +
373D LYS* 2.8 35.5 + - + +
374D VAL* 4.0 21.3 - - + -
375D ASN* 2.9 26.0 + - - -
376D ILE 4.8 0.2 + - - -
398D LEU* 4.7 0.2 - - - -
409D LEU* 3.4 47.1 - - + -
411D SER* 5.7 0.7 - - - -
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Residues in contact with GLU 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D MET* 5.4 3.1 - - - +
350D TRP* 1.3 71.6 - - - +
352D VAL* 1.3 57.2 + - - +
353D ASN 3.9 0.4 + - - -
375D ASN* 3.4 26.7 - - - +
376D ILE* 4.4 3.8 + - - +
377D ASN 5.0 0.2 + - - -
378D GLY 4.5 8.5 - - - +
379D GLY* 5.6 0.3 - - - -
393D ARG* 4.6 4.9 + - - -
394D ILE* 3.5 40.0 - - + +
397D HIS* 3.2 29.8 - - + -
398D LEU* 3.6 28.9 - - + +
409D LEU 2.9 9.8 + - - -
410D ALA* 3.2 11.4 - - + +
411D SER 2.8 33.3 + - - +
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Residues in contact with VAL 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D PRO* 5.1 2.7 - - + -
350D TRP* 3.9 21.5 - - + -
351D GLU* 1.3 72.6 - - - +
353D ASN* 1.3 72.7 + - - +
354D GLU 3.2 0.3 + - - -
359D VAL* 4.7 4.5 - - + +
360D VAL* 3.6 15.5 - - + +
363D ASN* 4.0 35.4 - - + +
364D ILE* 6.3 0.7 - - + -
367D LEU* 5.8 2.5 - - + -
369D ILE* 6.0 3.1 - - + -
374D VAL* 4.2 17.0 - - + -
375D ASN* 2.8 37.1 + - - +
409D LEU 5.6 0.2 - - - +
411D SER* 3.6 21.8 - - - +
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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