Contacts of the strand formed by residues 328 - 332 (chain A) in PDB entry 2IFG
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 ILE 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A LEU* 3.8 34.1 - - + -
323A ASN 5.1 1.8 - - - +
324A GLU* 3.0 8.5 - - + -
325A THR* 2.8 33.0 + - + +
327A PHE* 1.3 88.0 - - + +
329A PHE* 1.3 61.3 + - - +
346A LEU* 3.8 13.2 - - + -
347A ARG 3.2 3.4 - - - -
348A LEU* 3.4 31.4 - - + -
349A ASN 5.3 0.2 - - - +
351A PRO* 5.8 1.6 - - + -
355A ASN* 3.5 29.4 - - + +
359A TYR* 5.2 2.2 - - - +
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A HIS* 4.5 13.0 - + - -
324A GLU* 3.7 15.5 - - + +
325A THR 3.5 10.3 - - - +
326A SER* 3.3 28.0 - - - -
327A PHE 3.9 4.0 - - - -
328A ILE* 1.3 80.7 - - - +
330A THR* 1.3 69.6 + - - +
331A GLU* 4.5 11.9 - - + -
346A LEU* 3.8 6.1 - - - -
347A ARG* 2.8 77.5 + - + +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A PHE* 3.8 24.2 - - + -
313A LEU* 4.2 12.1 - - + +
315A TRP* 2.9 32.2 + - - +
324A GLU* 3.1 23.6 + - - +
329A PHE* 1.3 80.9 - - - +
331A GLU* 1.3 65.3 + - - +
332A PHE* 4.1 22.1 - - + -
345A CYS 3.5 4.9 - - - +
346A LEU* 4.4 1.5 - - - +
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A PHE* 3.8 1.1 - - - -
329A PHE* 4.5 10.7 - - + -
330A THR* 1.3 76.8 - - - +
332A PHE* 1.3 76.5 + - - +
333A LEU* 5.4 2.0 - - + +
344A GLY* 2.9 4.9 - - - -
345A CYS* 2.7 41.6 + - + +
347A ARG* 2.6 54.7 + - + -
11E GLU* 4.4 2.4 - - - +
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Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A PHE* 3.9 15.3 - + - -
305A VAL* 4.7 3.6 - - + -
311A PRO 5.6 2.9 - - - -
313A LEU* 3.4 32.8 - - + -
330A THR* 4.1 14.1 - - + -
331A GLU* 1.3 91.0 - - - +
333A LEU* 1.3 63.0 + - - +
342A ARG* 2.9 61.9 - - + +
343A HIS 3.6 4.5 - - - -
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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