Contacts of the strand formed by residues 413 - 418 (chain C) in PDB entry 1U7V
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 THR 413 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A SER* 6.0 0.3 - - - -
360C PRO* 3.6 14.6 - - - +
409C THR 3.5 9.8 + - - -
410C ARG* 3.2 21.1 + - - +
411C MET 3.2 3.0 - - - +
412C CYS* 1.3 82.0 - - - +
414C ILE* 1.3 75.9 + - - +
415C ARG* 4.3 9.2 - - + +
439C GLU* 3.1 40.6 - - + +
440C LEU 3.2 4.5 - - - +
441C HIS* 3.4 16.8 + - - -
446C LEU* 6.0 0.5 - - - +
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Residues in contact with ILE 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C VAL* 5.4 0.4 - - + -
357C VAL* 3.8 26.9 - - + -
358C GLN 3.9 4.9 - - - +
359C SER* 4.1 15.5 - - - +
384C ILE* 3.6 41.5 - - + +
385C PHE* 3.9 19.7 - - + -
413C THR* 1.3 84.7 - - - +
415C ARG* 1.3 65.2 + - - +
416C MET* 4.2 6.9 + - + +
438C ILE 3.8 0.9 - - - +
439C GLU* 3.5 2.4 - - - -
440C LEU* 2.8 51.1 + - + +
442C LEU* 4.1 16.6 - - + -
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Residues in contact with ARG 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 4.8 8.3 - - - -
318A ASN 5.9 0.8 - - - -
319A VAL* 4.5 17.6 - - - +
357C VAL* 3.5 1.9 - - - -
358C GLN* 2.8 61.4 + - + +
413C THR* 4.3 6.9 - - + +
414C ILE* 1.3 77.9 - - - +
416C MET* 1.3 61.7 + - - +
422C TRP* 3.6 12.5 - - + -
431C VAL* 3.9 26.1 - - + +
437C TRP* 3.8 26.1 - - + -
438C ILE 3.5 4.5 - - - +
439C GLU* 3.0 33.8 + - + -
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Residues in contact with MET 416 (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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336C VAL* 3.4 44.0 - - + -
338C LEU* 4.0 20.6 - - - -
347C ALA* 4.6 5.2 - - + -
355C ILE* 3.7 19.3 - - + -
356C PHE 3.1 5.6 - - - +
357C VAL* 3.8 25.8 - - + -
384C ILE* 4.9 5.6 - - - -
414C ILE* 4.6 6.1 - - + +
415C ARG* 1.3 79.2 - - - +
417C SER* 1.3 61.3 + - - +
418C PHE* 4.7 6.4 - - + -
422C TRP* 4.4 1.6 - - - -
437C TRP* 3.0 5.3 - - - +
438C ILE* 2.7 54.3 + - + +
440C LEU* 4.8 7.0 - - - -
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Residues in contact with SER 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ILE* 3.3 8.8 - - - +
356C PHE* 2.9 30.5 + - - -
416C MET* 1.3 76.6 - - - +
418C PHE* 1.3 65.4 + - - +
420C LYS 2.6 27.3 + - - -
422C TRP* 3.6 25.7 - - - -
434C THR* 3.4 20.9 - - - -
436C CYS 3.5 6.4 + - - -
437C TRP* 3.9 4.3 - - - -
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Residues in contact with PHE 418 (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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299C VAL* 3.9 19.1 - - + -
313C LEU* 3.9 24.7 - - + -
328C THR* 3.6 9.4 - - - +
332C ILE* 4.0 33.4 - - + -
335C GLY* 4.1 5.2 - - - -
336C VAL* 3.5 46.0 - - + -
351C SER* 5.4 1.6 - - - -
354C ALA 4.3 1.3 - - - -
355C ILE* 3.8 17.5 - - + -
416C MET* 4.7 7.2 - - + -
417C SER* 1.3 75.6 + - - +
419C VAL* 1.3 60.7 + - + +
420C LYS* 2.7 18.6 + - - +
436C CYS* 2.7 31.9 + - + +
437C TRP* 4.7 1.8 - - - -
438C ILE* 4.5 18.8 - - + -
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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