Contacts of the strand formed by residues 342 - 348 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B PHE* 4.0 0.6 - - - +
304B SER* 3.3 3.8 - - - -
305B VAL* 2.9 49.8 + - + +
332B PHE* 3.2 49.6 - - + +
333B LEU 3.8 8.8 + - - -
335B PRO* 2.9 53.0 - - - +
340B THR 3.7 10.8 - - - +
341B VAL* 1.3 79.2 - - - +
343B HIS* 1.3 63.7 + - - +
2M NDG 6.6 0.4 - - - -
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Residues in contact with HIS 343 (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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303B PHE* 3.3 9.4 - - - -
304B SER* 2.8 29.2 + - - -
332B PHE* 3.7 8.1 - - - -
333B LEU* 2.9 37.8 + - + +
336B ALA* 6.1 2.2 - - + -
339B GLU* 4.5 8.1 + - - -
341B VAL* 3.6 38.0 - - + +
342B ARG* 1.3 75.5 + - - +
344B GLY* 1.3 58.7 - - - +
4F HIS* 3.6 15.1 + + + -
5F PRO* 3.5 28.1 - - + +
9F ARG* 5.6 3.8 - - - -
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Residues in contact with GLY 344 (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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302B PRO* 3.3 6.2 - - - +
303B PHE* 3.0 37.7 + - - +
331B GLU 3.2 13.2 - - - -
333B LEU* 4.1 11.2 - - - -
343B HIS* 1.3 76.8 - - - +
345B CYS* 1.3 65.7 + - - +
4F HIS* 3.6 8.7 - - - -
6F ILE* 5.2 0.2 - - - -
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Residues in contact with CYS 345 (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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300B CYS* 2.0 49.6 - - + -
301B ILE 3.2 8.3 - - - -
303B PHE* 3.2 11.1 - - - -
330B THR* 3.5 2.4 - - - -
331B GLU* 2.9 31.6 + - + +
344B GLY* 1.3 72.1 - - - -
346B LEU* 1.3 62.9 + - - +
347B ARG* 3.6 13.9 + - + -
6F ILE* 3.4 31.6 - - - -
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Residues in contact with LEU 346 (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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300B CYS* 3.3 1.9 - - - -
301B ILE* 3.0 41.3 + - + -
315B TRP* 3.5 39.6 - - + -
322B LEU* 4.2 6.3 - - + -
324B GLU* 5.3 2.5 - - + -
328B ILE* 3.8 17.0 - - + -
329B PHE* 3.6 23.3 - - - +
330B THR* 4.2 8.3 - - - +
345B CYS* 1.3 72.4 - - - +
347B ARG* 1.3 56.6 + - - +
348B LEU* 3.1 19.6 - - + +
359B TYR* 3.5 37.9 - - + -
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Residues in contact with ARG 347 (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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297B HIS* 4.1 6.5 - - - +
298B HIS* 3.3 46.7 + - + +
299B TRP 3.5 7.9 - - - +
300B CYS* 5.1 0.7 - - + -
327B PHE 3.6 1.4 - - - +
328B ILE* 3.3 5.7 - - - -
329B PHE* 2.7 55.5 + - + +
331B GLU* 2.7 56.3 + - + -
345B CYS* 3.5 21.5 - - + -
346B LEU* 1.3 72.6 - - - +
348B LEU* 1.3 61.5 + - - +
349B ASN 4.1 0.7 - - - -
79E TYR* 5.1 1.4 + - - -
11F GLU* 2.8 36.0 + - - +
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Residues in contact with LEU 348 (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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298B HIS* 3.8 3.9 - - - +
299B TRP* 3.0 40.8 + - + +
301B ILE* 4.2 14.8 - - + -
327B PHE 3.4 1.8 - - - -
328B ILE* 3.3 45.5 - - + -
346B LEU* 3.1 36.3 - - + +
347B ARG* 1.3 73.4 - - - +
349B ASN* 1.3 60.8 + - - +
350B GLN 3.3 5.5 + - - -
351B PRO* 3.5 23.4 - - + +
359B TYR* 4.9 7.4 - - + +
378B PHE* 4.3 17.3 - - + -
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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