Contacts of the helix formed by residues 308 - 313 (chain B) in PDB entry 3IFS
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 SER 308 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ILE* 4.3 1.0 - - - +
120A ASN* 4.3 6.0 - - - +
121A ILE* 3.7 19.5 - - - +
151A GLU* 2.7 37.0 + - - +
425A TYR* 5.6 0.9 - - - -
429A MSE 6.4 0.2 - - - -
274B TYR* 4.1 10.0 - - - -
307B PHE* 1.3 75.8 + - - +
309B THR* 1.3 67.5 + - - +
310B ASP 3.3 2.2 - - - -
311B LEU* 2.9 33.1 + - - +
312B HIS* 3.4 6.6 - - - -
363B ASN* 4.9 2.6 + - - -
366B ALA* 5.0 3.4 - - - -
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Residues in contact with THR 309 (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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82A ILE* 4.2 5.4 - - + +
83A GLY* 5.1 1.8 + - - +
86A TYR* 4.0 29.2 - - + +
87A LEU* 5.8 2.7 - - + -
119A GLN* 2.6 34.1 + - + +
120A ASN* 3.7 11.4 - - - +
306B ASN* 3.3 16.0 + - + +
307B PHE 3.2 2.7 + - - -
308B SER* 1.3 77.4 + - - +
310B ASP* 1.3 68.9 + - - +
312B HIS* 3.1 25.1 + - - +
313B SER* 4.2 1.6 + - - -
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Residues in contact with ASP 310 (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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87A LEU* 6.0 1.6 - - - +
283A GLU* 4.5 14.9 - - - +
305B ALA* 3.5 12.1 - - + +
306B ASN* 2.8 50.4 + - - +
307B PHE* 4.0 16.7 - - + -
309B THR* 1.3 82.2 - - - +
311B LEU* 1.3 56.2 + - - +
312B HIS 3.0 5.8 - - - -
313B SER* 3.3 18.0 + - - +
314B LEU* 2.8 36.2 + - + +
315B GLY 3.1 4.0 + - - -
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Residues in contact with LEU 311 (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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291A GLU* 4.9 0.2 - - - +
422A VAL* 3.9 15.1 - - - +
425A TYR* 3.7 39.6 - - + +
274B TYR* 4.6 3.1 - - + +
307B PHE* 3.7 39.9 - - + -
308B SER* 2.9 30.4 + - - +
310B ASP* 1.3 78.8 - - - +
312B HIS* 1.3 58.0 + - - +
313B SER 3.4 1.1 - - - -
315B GLY* 3.3 25.2 + - - -
316B GLN 4.4 0.2 + - - -
366B ALA* 5.4 1.3 - - + +
370B THR* 3.5 26.9 - - + +
374B HIS* 3.8 19.7 - - + +
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Residues in contact with HIS 312 (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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82A ILE* 3.2 30.1 - - + +
83A GLY* 3.7 19.8 - - - -
149A THR* 3.8 28.9 - - + +
151A GLU* 2.9 22.4 + - - -
287A GLN* 3.1 27.2 + - - +
291A GLU* 3.5 12.0 - - - +
422A VAL* 5.5 1.3 - - - -
425A TYR* 3.2 19.7 + - - -
426A LYS* 4.6 10.2 + - - -
308B SER 3.4 13.0 - - - -
309B THR 3.1 7.6 + - - +
310B ASP 3.0 0.8 - - - -
311B LEU* 1.3 80.0 - - - +
313B SER* 1.3 56.3 + - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 6.0 0.2 - - - -
87A LEU* 4.1 15.7 - - - +
283A GLU* 4.8 4.8 + - - -
286A LYS* 5.6 1.1 - - - +
287A GLN* 3.6 36.8 - - - -
291A GLU* 3.3 27.4 + - - +
309B THR 5.0 0.4 - - - -
310B ASP* 3.3 28.8 + - - +
311B LEU 3.4 0.4 - - - -
312B HIS* 1.3 81.3 - - - +
314B LEU* 1.3 74.4 + - - +
315B GLY 3.6 0.7 - - - -
316B GLN 5.0 0.2 + - - -
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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