Contacts of the strand formed by residues 268 - 273 (chain C) 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 ILE 268 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266C LYS 3.4 0.2 - - - -
267C THR* 1.3 87.6 - - - +
269C GLU* 1.3 64.9 + - - +
270C MSE 4.2 4.3 - - + -
300C ILE* 4.2 0.7 - - - -
301C PHE* 3.5 12.3 - - + +
303C SER* 4.1 20.4 - - - -
317C TYR* 5.9 0.4 - - - +
324C ASP* 3.0 13.7 + - + +
325C LEU* 3.3 34.3 - - + -
326C PHE* 3.0 30.0 + - - +
267D THR* 5.6 0.7 - - - +
268D ILE* 3.8 33.4 - - + -
301D PHE* 3.8 24.7 - - + -
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Residues in contact with GLU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C TYR* 2.6 24.2 + - - -
258C ARG* 2.8 33.7 + - - -
268C ILE* 1.3 72.5 - - - +
270C MSE 1.3 66.3 + - - +
285C TRP* 3.5 21.1 - - + -
300C ILE* 3.5 15.6 - - + +
301C PHE 3.0 7.5 + - - +
302C PRO* 3.7 1.0 - - - +
303C SER* 2.8 29.8 + - - +
326C PHE* 3.4 29.8 - - + +
328C THR* 2.7 24.5 + - - +
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Residues in contact with MSE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C ILE* 4.2 9.4 - - + -
269C GLU* 1.3 77.4 - - - +
271C LEU* 1.3 60.8 + - - +
272C ILE* 3.4 16.6 + - + +
303C SER* 3.4 22.9 - - - +
304C SER* 4.7 3.1 - - - +
305C ALA* 3.6 31.9 - - + +
307C PHE* 4.6 1.6 - - + -
314C LEU* 4.8 10.3 - - + -
318C VAL* 3.7 33.4 - - + -
325C LEU* 4.2 11.2 - - + -
326C PHE 2.9 14.5 + - - +
327C GLU* 3.3 12.2 - - + +
328C THR 3.1 22.2 + - - -
301D PHE* 4.0 19.7 - - + -
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C GLU 3.9 1.0 + - - -
270C MSE 1.3 68.9 - - - +
272C ILE* 1.3 59.3 + - - +
273C ASN* 5.8 0.2 + - - -
281C PHE* 4.7 4.0 - - + -
282C ALA* 3.8 22.7 - - + +
285C TRP* 3.6 60.9 - - + +
303C SER 2.9 9.7 + - - +
304C SER* 3.2 6.9 - - - -
305C ALA 3.0 23.4 + - - +
328C THR* 3.4 33.9 - - + +
330C LEU* 4.0 35.2 - - + -
401C PHE* 4.5 3.4 - - + -
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Residues in contact with ILE 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C MSE 3.5 33.0 - - + +
271C LEU* 1.3 76.3 - - - +
273C ASN* 1.3 67.3 + - - +
274C TYR* 3.9 12.3 - - + -
305C ALA* 3.5 9.4 - - + +
307C PHE* 3.3 42.2 - - + -
327C GLU* 3.5 35.0 - - + +
328C THR 2.8 13.2 + - - +
329C VAL* 4.0 12.1 - - + -
330C LEU* 2.8 35.4 + - - +
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Residues in contact with ASN 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C LEU 5.8 0.4 + - - -
272C ILE* 1.3 74.9 - - - +
274C TYR* 1.3 61.0 + - - +
275C GLU 3.0 28.9 + - - +
276C PRO* 4.0 0.4 - - - +
278C LEU* 3.8 44.2 + - + +
279C GLN* 3.8 1.0 - - - +
282C ALA* 5.2 4.8 - - - +
305C ALA 3.3 5.9 + - - -
306C ASN* 2.9 37.1 + - - +
307C PHE* 2.8 35.0 + - - +
330C LEU* 4.1 10.5 - - + -
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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