Contacts of the helix formed by residues 383 - 393 (chain C) in PDB entry 3GZN
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 SER 383 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380C GLU 5.1 3.6 - - - -
381C SER 3.9 4.0 + - - -
382C ILE* 1.3 78.3 - - - +
384C GLU* 1.3 59.1 + - - +
385C LYS* 3.9 11.6 + - - +
386C GLU* 2.8 42.4 + - - +
387C LEU* 2.9 24.5 + - - +
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Residues in contact with GLU 384 (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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382C ILE 4.0 0.4 + - - -
383C SER* 1.3 70.7 - - - +
385C LYS* 1.3 60.6 + - - +
386C GLU 3.1 0.7 - - - -
387C LEU* 3.6 15.9 - - + +
388C LYS* 2.9 32.7 + - - +
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Residues in contact with LYS 385 (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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30C HIS* 5.1 14.4 - - - +
383C SER* 3.9 11.6 + - - +
384C GLU* 1.3 78.4 - - - +
386C GLU* 1.3 60.8 + - + +
388C LYS* 4.0 16.4 - - + +
389C LEU* 4.1 14.9 + - - +
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Residues in contact with GLU 386 (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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310C SER* 5.1 4.0 + - - -
314C LEU* 5.4 5.2 - - + +
381C SER 4.9 3.0 - - - +
382C ILE* 4.0 20.5 - - + +
383C SER* 2.8 36.2 + - - +
385C LYS* 1.3 76.8 - - + +
387C LEU* 1.3 63.8 + - - +
388C LYS 3.4 0.7 - - - -
389C LEU* 3.7 11.8 + - + +
390C LEU* 3.4 20.8 + - - +
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Residues in contact with LEU 387 (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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314C LEU* 4.3 12.8 - - + -
361C ALA* 3.4 36.1 - - + +
362C ALA* 4.6 2.7 - - - +
364C VAL* 4.2 15.5 - - + -
365C GLY* 3.7 13.0 - - - -
368C VAL* 4.0 26.9 - - + -
382C ILE* 5.0 5.6 - - + +
383C SER 2.9 12.5 + - - +
384C GLU* 3.1 17.0 + - + +
386C GLU* 1.3 77.3 - - - +
388C LYS* 1.3 64.6 + - - +
390C LEU* 3.5 5.8 + - + +
391C CYS* 3.1 25.2 + - - +
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Residues in contact with LYS 388 (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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354C ARG* 3.2 31.9 - - - +
358C LYS* 5.7 9.0 - - + -
361C ALA* 5.5 4.2 - - - +
384C GLU 2.9 14.8 + - - +
385C LYS* 4.0 11.0 - - + +
387C LEU* 1.3 75.8 - - - +
389C LEU* 1.3 55.4 + - + +
391C CYS* 3.0 6.6 + - - +
392C SER* 2.8 36.3 + - - -
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Residues in contact with LEU 389 (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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30C HIS* 4.6 17.0 - - + +
179C ILE* 4.0 10.9 - - + +
180C GLU* 4.1 30.7 - - + +
385C LYS 4.2 12.8 - - - +
386C GLU* 3.7 13.4 + - + +
387C LEU 3.4 0.4 - - - -
388C LYS* 1.3 79.8 - - + +
390C LEU* 1.3 58.0 + - - +
392C SER* 4.3 4.0 - - - -
393C ASN* 2.7 51.4 + - - +
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Residues in contact with LEU 390 (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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179C ILE* 4.1 21.0 - - + +
311C PHE* 5.5 2.2 - - + +
314C LEU* 3.5 52.9 - - + +
315C ALA 5.1 0.9 - - - +
318C LEU* 3.8 31.1 - - + +
364C VAL* 4.5 11.7 - - + -
386C GLU 3.4 14.3 + - - +
387C LEU* 3.9 4.9 - - + +
388C LYS 3.3 0.8 - - - -
389C LEU* 1.3 78.3 - - - +
391C CYS* 1.3 59.8 + - - +
393C ASN 3.5 1.2 - - - -
394C SER* 3.0 26.9 + - - -
397C LEU* 3.8 25.8 - - + -
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Residues in contact with CYS 391 (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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318C LEU* 4.7 3.6 - - - -
331C PRO* 4.3 20.2 - - + +
332C VAL 4.7 8.3 - - - +
333C ARG* 4.9 2.7 - - - -
357C ALA* 5.6 1.8 - - + +
361C ALA* 3.7 36.3 - - + -
364C VAL* 3.9 27.6 - - - -
387C LEU* 3.1 19.0 + - - +
388C LYS* 3.0 4.7 + - - +
390C LEU* 1.3 78.1 - - - +
392C SER* 1.3 66.6 + - - +
393C ASN 3.4 0.3 + - - -
394C SER* 3.4 18.9 + - - -
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Residues in contact with SER 392 (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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333C ARG* 3.9 41.7 + - - +
335C THR* 5.9 3.6 - - - +
388C LYS 2.8 21.1 + - - -
389C LEU* 3.7 9.9 - - - -
391C CYS* 1.3 74.0 - - - +
393C ASN* 1.3 68.4 + - - +
394C SER* 3.5 2.8 + - - -
395C ALA* 4.9 0.9 + - - +
396C PHE* 4.4 4.0 - - - -
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Residues in contact with ASN 393 (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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179C ILE* 3.4 24.3 - - + +
180C GLU* 4.1 17.1 - - - +
181C SER 5.1 1.0 + - - -
182C HIS 5.6 0.7 + - - -
183C PRO* 5.5 2.1 - - - +
389C LEU* 2.7 45.0 + - - +
390C LEU 3.5 4.3 - - - -
392C SER* 1.3 82.8 - - - +
394C SER* 1.3 60.9 + - - +
395C ALA 3.0 5.6 - - - -
396C PHE* 3.0 36.3 + - + +
397C LEU* 3.5 15.0 + - - +
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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