Contacts of the strand formed by residues 325 - 334 (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 LEU 325 (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* 3.7 9.2 + - - +
268C ILE* 3.3 48.5 - - + +
270C MSE 4.2 17.7 - - - -
317C TYR* 4.2 18.4 - - + +
318C VAL* 4.1 30.1 - - + +
322C ARG 4.1 8.3 - - - +
323C ARG* 3.5 10.7 - - - +
324C ASP* 1.3 80.8 - - + +
326C PHE* 1.3 65.1 + - - +
378C GLY 4.5 1.2 - - - +
379C VAL* 3.8 15.3 - - + +
380C PRO* 3.5 16.1 - - - +
301D PHE* 3.8 15.0 - - + -
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Residues in contact with PHE 326 (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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258C ARG* 4.2 13.5 - - + -
261C LEU* 3.7 23.6 - - + -
266C LYS* 3.8 28.3 - - + -
268C ILE 3.0 13.0 + - - +
269C GLU* 3.4 52.8 - - + -
270C MSE 2.9 25.8 + - - +
300C ILE* 4.1 18.4 - - + -
325C LEU* 1.3 74.4 - - - +
327C GLU* 1.3 67.4 + - - +
328C THR* 3.8 6.7 - - - -
379C VAL* 3.9 2.2 - - - -
380C PRO* 3.5 28.0 - - + +
382C LEU* 3.9 19.1 - - + -
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Residues in contact with GLU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C MSE 3.3 17.2 - - + +
272C ILE* 3.5 30.4 - - + +
307C PHE* 3.6 9.9 - - - -
318C VAL* 3.6 17.8 - - + +
325C LEU* 5.9 0.7 - - + -
326C PHE* 1.3 78.1 - - - +
328C THR* 1.3 58.5 + - - +
329C VAL* 4.0 1.1 - - + -
374C HIS* 2.8 34.8 + - - +
379C VAL* 3.6 7.5 - - + +
380C PRO 2.9 7.2 + - - +
381C ASN* 3.4 31.0 + - - +
382C LEU* 2.8 33.1 + - - +
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Residues in contact with THR 328 (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* 3.8 14.8 - - + +
269C GLU* 2.7 30.4 + - - +
270C MSE 3.1 7.7 + - - -
271C LEU* 3.4 24.1 - - + +
272C ILE* 2.8 29.8 + - - -
326C PHE* 3.8 0.7 - - - -
327C GLU* 1.3 73.9 + - - +
329C VAL* 1.3 56.8 + - - +
382C LEU* 3.3 25.0 - - + +
384C VAL* 4.0 25.4 - - + -
401C PHE* 5.2 0.7 - - + -
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Residues in contact with VAL 329 (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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272C ILE* 3.5 23.3 - - + +
274C TYR* 4.1 15.9 - - + -
327C GLU* 4.7 0.9 - - + -
328C THR* 1.3 75.4 - - - +
330C LEU* 1.3 74.4 + - - +
331C LYS* 3.4 2.4 + - + +
367C TYR* 3.7 37.0 - - + -
371C LEU* 5.2 3.6 - - + -
381C ASN* 3.8 22.9 - - + +
382C LEU 2.8 16.9 + - - +
383C ILE* 3.6 5.0 - - + +
384C VAL* 2.9 28.4 + - - +
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Residues in contact with LEU 330 (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* 4.0 31.4 - - + -
272C ILE 2.8 22.3 + - - +
273C ASN* 4.1 13.0 - - + -
274C TYR* 4.3 7.1 + - - +
278C LEU* 4.0 30.1 - - + +
281C PHE* 4.0 26.9 - - + -
282C ALA* 6.1 0.7 - - + -
329C VAL* 1.3 75.6 - - - +
331C LYS* 1.3 60.4 + - - +
332C VAL* 3.9 2.9 + - - +
384C VAL* 3.5 27.1 - - + -
386C ILE* 4.0 17.7 - - + -
401C PHE* 4.0 16.6 - - + -
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Residues in contact with LYS 331 (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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274C TYR* 5.7 6.5 - - + -
329C VAL* 3.4 1.5 + - + +
330C LEU* 1.3 73.8 - - - +
332C VAL* 1.3 88.1 + - - +
333C GLY* 3.7 8.2 + - - -
360C ASP* 5.5 1.6 + - - -
364C THR* 3.8 28.0 + - - +
367C TYR* 3.4 59.9 - - + -
383C ILE* 4.3 5.6 - - + -
384C VAL 3.0 8.0 + - - +
385C ASN* 3.6 22.4 - - - +
386C ILE* 2.8 28.1 + - - +
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Residues in contact with VAL 332 (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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275C GLU* 4.3 21.3 - - + +
278C LEU* 4.2 20.2 - - + -
330C LEU 3.9 2.2 + - - +
331C LYS* 1.3 96.7 + - - +
333C GLY* 1.3 64.9 + - - +
334C LYS 3.5 24.3 - - - +
335C SER* 5.2 2.5 - - - -
360C ASP* 5.2 4.2 - - - +
386C ILE* 3.2 14.8 - - + +
388C GLU* 4.4 5.4 - - - -
389C LEU* 4.0 38.8 - - + -
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Residues in contact with GLY 333 (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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331C LYS* 3.7 8.9 + - - -
332C VAL* 1.3 75.3 - - - +
334C LYS* 1.3 59.3 + - - +
335C SER 4.3 0.5 + - - -
360C ASP* 4.5 8.1 - - - +
386C ILE 2.8 15.1 + - - -
387C PRO* 3.4 10.7 + - - -
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Residues in contact with LYS 334 (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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332C VAL* 3.5 17.7 - - - +
333C GLY* 1.3 75.9 - - - +
335C SER* 1.3 94.8 + - - +
336C THR* 3.8 6.2 + - - -
338C GLU* 3.1 35.3 + - - +
360C ASP* 5.2 0.2 - - - -
387C PRO 2.9 15.4 + - - +
388C GLU* 4.3 18.6 - - + +
389C LEU* 4.8 2.3 + - - +
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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