Contacts of the strand formed by residues 342 - 348 (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 ARG 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A PHE* 4.4 0.8 - - - -
304A SER* 3.3 5.4 - - - -
305A VAL* 2.9 44.6 + - + +
310A ALA* 5.8 8.5 - - + -
332A PHE* 2.9 58.1 - - + +
333A LEU 3.0 21.2 + - - -
334A GLU 4.1 0.2 + - - -
335A PRO* 3.0 42.6 - - - +
340A THR 3.7 10.5 - - - +
341A VAL* 1.3 79.9 - - - +
343A HIS* 1.3 65.5 + - - +
2G NDG 5.9 7.4 - - - +
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Residues in contact with HIS 343 (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* 3.4 7.2 - - - -
304A SER* 3.2 23.7 + - - -
332A PHE* 3.6 5.9 - - - +
333A LEU* 2.9 36.8 + - + +
336A ALA* 6.1 2.0 - - + -
339A GLU* 4.1 9.5 + - - -
341A VAL* 3.6 39.9 - - + +
342A ARG* 1.3 77.0 + - - +
344A GLY* 1.3 59.5 + - - +
4E HIS* 4.0 3.8 - - + -
5E PRO* 3.4 39.5 - - + +
9E ARG* 6.3 0.9 - - - -
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Residues in contact with GLY 344 (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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302A PRO* 3.4 5.0 - - - +
303A PHE* 2.9 41.3 + - - +
331A GLU 2.9 13.7 - - - -
332A PHE* 4.0 0.7 - - - -
333A LEU* 4.2 9.9 - - - -
343A HIS* 1.3 75.7 - - - +
345A CYS* 1.3 63.4 + - - +
4E HIS* 3.8 7.3 - - - -
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Residues in contact with CYS 345 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A CYS* 2.0 50.3 - - + -
301A ILE 3.3 6.1 - - - -
302A PRO* 4.5 0.2 - - - -
303A PHE* 3.2 8.5 - - - -
330A THR* 3.5 1.4 - - - -
331A GLU* 2.7 41.3 + - + +
344A GLY* 1.3 74.3 - - - -
346A LEU* 1.3 62.4 + - - +
347A ARG* 3.4 15.6 + - + -
6E ILE* 3.5 29.6 - - - -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A CYS* 3.3 3.6 - - - -
301A ILE* 2.9 54.4 + - + -
315A TRP* 3.4 43.0 - - + +
322A LEU* 4.0 8.7 - - + -
324A GLU* 5.5 1.8 - - + -
328A ILE* 3.8 17.7 - - + -
329A PHE* 3.5 18.8 - - - +
330A THR* 4.3 3.8 - - - +
345A CYS* 1.3 72.1 - - - +
347A ARG* 1.3 61.5 + - - +
348A LEU* 3.2 19.5 - - + +
359A TYR* 3.5 25.6 - - + -
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Residues in contact with ARG 347 (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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297A HIS* 4.0 11.3 - - - -
298A HIS* 2.7 48.1 + - - +
299A TRP 3.6 6.1 - - - +
300A CYS* 5.0 1.3 - - + -
327A PHE 3.2 3.0 - - - +
328A ILE* 3.2 7.1 - - - -
329A PHE* 2.8 57.6 + - + +
331A GLU* 2.6 51.0 + - + -
345A CYS* 3.4 22.6 + - + -
346A LEU* 1.3 72.1 - - - +
348A LEU* 1.3 60.3 + - - +
11E GLU* 3.1 29.0 + - - +
79F TYR* 5.4 1.8 + - - -
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Residues in contact with LEU 348 (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* 3.6 3.3 - - - +
299A TRP* 2.8 55.4 + - + +
301A ILE* 4.0 16.2 - - + -
327A PHE 3.4 2.7 - - - -
328A ILE* 3.4 42.6 - - + -
346A LEU* 3.2 36.3 - - + +
347A ARG* 1.3 71.4 - - - +
349A ASN* 1.3 59.9 + - - +
350A GLN 3.3 5.2 + - - -
351A PRO* 3.9 15.5 - - + -
359A TYR* 4.8 9.4 - - - +
378A PHE* 4.2 17.5 - - + -
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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