Contacts of the strand formed by residues 364 - 371 (chain C) in PDB entry 4IG9
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 GLY 364 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346C ASN 3.9 1.0 - - - +
347C ILE* 3.4 18.0 - - - +
361C GLN* 2.6 33.6 + - - +
362C CYS 3.4 0.6 - - - -
363C HIS* 1.3 76.2 + - - +
365C SER* 1.3 63.9 + - - -
410C GLU* 3.0 14.1 - - - -
411C ILE* 3.9 3.8 - - - -
412C VAL* 3.9 5.7 - - - +
419C PRO* 5.2 3.6 - - - -
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Residues in contact with SER 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ILE* 4.4 2.2 - - - -
349C THR* 3.6 17.7 - - - -
361C GLN* 3.4 30.3 - - - +
364C GLY* 1.3 76.0 - - - -
366C PHE* 1.3 59.6 + - - +
367C ALA* 3.2 23.0 + - - +
368C THR 4.8 0.2 + - - -
410C GLU* 2.4 47.1 + - - +
411C ILE* 3.6 12.8 - - - +
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Residues in contact with PHE 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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309C PHE* 4.2 16.6 - + - -
312C PHE* 4.4 12.3 - + - -
313C ALA* 3.7 34.3 - - + -
316C ILE* 4.9 13.7 - - + -
317C TYR* 3.9 31.6 + + + -
318C PRO* 4.2 10.1 - - + -
347C ILE* 3.3 31.0 - - + -
348C ASP* 5.3 0.7 - - - -
349C THR* 3.1 15.2 - - + +
365C SER* 1.3 74.2 - - - +
367C ALA* 1.3 62.8 + - - +
368C THR 3.2 8.8 + - - +
380C CYS* 3.4 20.4 - - - +
409C PRO* 3.7 29.8 - - + +
411C ILE* 3.9 11.4 - - + -
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Residues in contact with ALA 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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349C THR* 4.1 3.8 - - - +
352C GLN* 3.8 33.0 - - + +
365C SER* 3.2 17.9 + - - +
366C PHE* 1.3 78.4 - - - +
368C THR* 1.3 70.2 + - + +
379C ASP* 4.3 1.6 - - - +
380C CYS* 3.1 30.2 + - - +
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Residues in contact with THR 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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365C SER 3.8 2.7 + - - +
366C PHE 4.0 4.8 - - - -
367C ALA* 1.3 88.4 - - + +
369C ALA* 1.3 56.6 + - - +
377C LYS* 3.9 22.4 - - + +
378C VAL 3.1 21.1 - - - +
379C ASP* 4.2 8.7 - - - +
380C CYS* 5.6 0.4 - - - -
409C PRO* 3.5 3.3 - - - +
410C GLU* 2.8 57.9 + - - +
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Residues in contact with ALA 369 (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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368C THR* 1.3 77.2 - - - +
370C SER* 1.3 62.7 + - - +
376C TYR 3.4 1.6 - - - +
377C LYS* 3.2 4.5 - - - -
378C VAL* 2.9 37.8 + - + +
379C ASP 4.6 0.2 + - - -
383C VAL* 3.9 28.3 - - + -
407C MET* 3.6 12.5 - - + +
408C LYS 3.4 13.5 - - - +
409C PRO* 3.7 11.2 - - + -
410C GLU* 4.1 1.6 - - - +
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Residues in contact with SER 370 (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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369C ALA* 1.3 75.8 - - - +
371C CYS* 1.3 68.6 + - - +
372C LEU* 3.8 0.7 + - - +
375C LYS* 3.2 34.8 + - - +
376C TYR 3.3 6.3 - - - -
377C LYS* 4.3 10.6 - - - +
407C MET* 4.3 1.1 - - - -
408C LYS* 2.6 39.3 + - - +
409C PRO 4.8 0.2 - - - -
410C GLU* 4.5 14.1 - - - +
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Residues in contact with CYS 371 (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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370C SER* 1.3 77.3 + - - +
372C LEU* 1.3 69.2 + - - +
373C ILE* 3.1 16.8 - - - -
375C LYS* 3.2 33.1 - - - +
376C TYR 3.4 9.6 + - - +
395C CYS* 3.9 10.8 - - - -
405C ALA* 4.0 10.3 - - - -
406C ILE 3.3 13.9 - - - +
407C MET* 3.7 19.9 - - - -
601C ZN 2.5 35.7 - - - -
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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