Contacts of the strand formed by residues 360 - 368 (chain C) in PDB entry 3F7F
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 ALA 360 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C TRP* 4.2 14.1 - - + -
356C LYS* 3.5 5.7 - - - +
357C SER* 3.0 35.8 + - - +
358C GLY 3.2 0.6 - - - -
359C THR* 1.3 81.3 + - - +
361C SER* 1.3 61.0 + - - +
384C LYS* 6.6 0.4 - - - +
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Residues in contact with SER 361 (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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6C ARG* 4.2 13.5 + - - +
329C TRP* 4.0 7.2 - - - -
354C LEU* 4.5 6.0 - - - +
355C TRP 3.6 10.8 - - - -
356C LYS* 5.0 0.4 - - - -
359C THR 4.1 1.9 + - - -
360C ALA* 1.3 76.5 - - - +
362C LYS* 1.3 63.6 + - - +
383C ASN* 3.3 23.0 + - - +
458C ASN 6.1 0.2 - - - -
460C ALA* 4.1 24.9 - - - +
484C TYR* 3.6 19.2 + - - -
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Residues in contact with LYS 362 (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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322C ASN 5.5 1.2 + - - -
323C LEU* 3.9 23.3 - - + -
329C TRP* 3.8 38.8 - - + +
353C VAL 3.6 1.0 - - - +
354C LEU* 3.5 4.8 - - - +
355C TRP* 2.8 47.9 + - + +
361C SER* 1.3 78.0 - - - +
363C LEU* 1.3 62.0 + - - +
364C GLN* 4.2 7.3 - - + +
380C GLU* 2.7 32.1 + - - +
383C ASN* 3.5 18.1 - - - +
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Residues in contact with LEU 363 (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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4C LEU* 4.4 13.7 - - + -
352C ILE* 4.0 13.0 - - + -
353C VAL 3.3 6.3 - - - +
354C LEU* 4.2 20.0 - - + -
362C LYS* 1.3 75.5 - - - +
364C GLN* 1.3 75.5 + - - +
365C ILE* 4.8 1.6 - - + -
380C GLU* 5.1 0.2 - - - +
381C SER* 3.0 43.3 + - - +
383C ASN* 3.1 8.8 + - - +
463C ILE* 5.1 2.0 - - + -
471C ILE* 3.7 29.8 - - + -
473C VAL* 4.4 5.2 - - + -
484C TYR* 3.8 40.4 - - + -
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Residues in contact with GLN 364 (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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321C THR* 6.0 0.7 - - - -
322C ASN* 3.5 29.4 + - - +
323C LEU* 4.2 6.2 - - - +
352C ILE* 3.6 1.0 - - - -
353C VAL* 2.8 32.9 + - + +
355C TRP* 2.7 36.2 + - + +
362C LYS* 4.2 9.1 - - + +
363C LEU* 1.3 85.1 - - - +
365C ILE* 1.3 69.4 + - - +
366C LEU 4.3 0.2 - - - -
378C TRP* 3.8 23.2 - - + -
379C ILE 3.4 12.8 - - - +
380C GLU* 3.0 34.7 + - - +
381C SER* 5.9 0.2 - - - -
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Residues in contact with ILE 365 (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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4C LEU* 3.9 21.5 - - + -
340C LEU* 3.8 21.1 - - + -
342C LEU* 4.1 12.1 - - + -
350C ASN* 3.4 34.1 - - + +
351C LEU 3.2 9.4 - - - +
352C ILE* 4.2 7.9 - - + -
363C LEU* 4.8 2.7 - - + -
364C GLN* 1.3 80.7 - - - +
366C LEU* 1.3 61.8 + - - +
367C ASN 3.6 1.6 + - - -
378C TRP* 3.7 3.4 - - - -
379C ILE* 3.0 40.8 + - + +
471C ILE* 3.5 33.0 - - + -
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Residues in contact with LEU 366 (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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298C PHE* 5.1 1.6 - - + -
300C MET* 3.9 17.0 - - + -
319C ILE* 3.8 31.2 - - + -
349C LEU 3.9 0.2 - - - +
350C ASN* 3.4 5.5 - - - -
351C LEU* 2.6 55.4 + - + +
365C ILE* 1.3 71.2 - - - +
367C ASN* 1.3 61.9 + - - +
368C VAL* 3.9 13.8 + - + +
376C TYR* 3.8 21.3 - - + -
377C GLU 4.0 2.7 - - - +
378C TRP* 3.3 49.0 - - + +
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Residues in contact with ASN 367 (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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342C LEU* 4.1 21.3 - - + +
344C VAL* 4.5 16.7 + - - +
346C ALA 3.4 19.3 + - - -
347C SER* 2.8 33.6 + - - -
350C ASN* 3.2 13.8 - - - +
365C ILE 3.6 0.8 + - - -
366C LEU* 1.3 72.6 - - - +
368C VAL* 1.3 62.3 + - - +
369C ASN* 4.4 6.7 + - - +
376C TYR* 3.2 4.8 - - - +
377C GLU* 2.8 50.8 + - - +
379C ILE* 4.8 5.6 - - + +
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Residues in contact with VAL 368 (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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300C MET* 4.4 22.4 - - - -
319C ILE* 4.5 3.1 - - + -
336C LEU* 6.5 0.7 - - + -
347C SER* 3.6 1.6 - - - -
348C TYR* 2.8 41.8 + - + -
349C LEU* 3.2 43.1 + - + +
351C LEU* 6.3 0.7 - - + -
366C LEU* 4.4 14.4 - - + +
367C ASN* 1.3 74.2 - - - +
369C ASN* 1.3 55.5 + - - +
370C ASP 4.6 5.2 - - - +
373C PHE* 4.6 13.7 - - + -
375C ASN 3.8 6.1 - - - +
376C TYR* 4.0 11.2 - - + -
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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