Contacts of the helix formed by residues 393 - 404 (chain C) in PDB entry 1G3I
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 393 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C GLY 3.0 9.2 + - - +
336C LEU* 4.1 9.5 - - + +
341C PHE* 3.8 14.5 - - + -
344C ILE* 5.3 2.7 - - + -
392C GLY* 1.3 67.4 - - - -
394C ARG* 1.3 67.0 + - - +
395C ARG 2.9 2.9 - - - -
396C LEU* 2.8 27.5 + - + +
397C HIS* 4.0 4.6 - - - -
452C ATP 3.1 47.1 - - + +
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Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLY* 4.8 2.6 + - - -
391C ILE* 3.4 29.3 + - + +
392C GLY 3.2 1.0 - - - -
393C ALA* 1.3 77.6 - - - +
395C ARG* 1.3 55.3 + - - +
396C LEU 2.6 12.6 + - - -
397C HIS* 2.7 54.8 + - - +
398C THR* 3.1 8.8 + - - -
452C ATP 4.2 30.3 + - - -
49D THR* 5.4 4.2 + - - -
287D GLU* 4.9 5.9 - - - +
321D PRO 5.7 1.1 - - - +
322D GLU* 5.2 5.6 + - - +
325D GLY* 4.2 21.9 + - - +
326D ARG* 3.4 44.5 - - - +
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Residues in contact with ARG 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C PHE* 5.1 0.2 - - + -
381C ALA* 3.6 28.0 - - + +
384C VAL* 3.5 36.3 - - + +
385C ASN* 2.8 27.8 + - - +
388C THR* 3.7 7.5 + - - -
389C GLU* 2.8 32.3 + - - +
391C ILE* 3.6 25.4 - - + +
392C GLY 3.4 10.8 + - - +
393C ALA 2.9 0.6 - - - -
394C ARG* 1.3 78.4 - - - +
396C LEU* 1.3 56.4 + - - +
398C THR* 3.4 24.8 + - - +
399C VAL* 2.9 28.1 + - + +
402C ARG* 5.9 0.2 - - - +
324D GLN* 4.8 9.7 + - - +
330D ARG* 5.9 2.2 - - - +
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Residues in contact with LEU 396 (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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341C PHE* 3.6 39.0 - - + +
344C ILE* 4.1 22.9 - - + -
345C LEU* 4.1 26.0 - - + +
352C LEU* 3.5 19.1 - - + -
377C ILE* 5.0 4.3 - - + +
378C ALA* 4.6 1.6 - - - -
381C ALA* 3.2 28.5 - - + -
393C ALA* 2.8 18.0 + - + +
394C ARG 2.6 5.5 + - - -
395C ARG* 1.3 71.3 - - - +
397C HIS* 1.3 57.6 + - + +
398C THR 3.0 1.3 + - - -
399C VAL* 3.1 2.5 + - + +
400C MET* 2.7 37.9 + - - +
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Residues in contact with HIS 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C LEU* 4.0 34.7 - - + +
355C GLN* 5.2 4.7 - - - -
356C TYR* 4.7 1.2 + - - -
393C ALA 4.0 10.8 - - - -
394C ARG* 2.7 49.9 + - - +
396C LEU* 1.3 72.8 - - + +
398C THR* 1.3 59.4 + - - +
400C MET* 4.0 2.3 - - - +
401C GLU* 3.2 25.1 + - - +
452C ATP 4.4 19.2 + - - -
49D THR* 5.3 5.5 + - - -
51D LYS* 4.3 18.2 + - + +
325D GLY 5.2 5.6 - - - +
328D PRO* 4.7 8.2 - - + +
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Residues in contact with THR 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ILE* 4.4 10.4 - - - +
394C ARG 3.1 6.6 + - - -
395C ARG* 3.4 39.1 + - - +
396C LEU 3.0 0.2 - - - -
397C HIS* 1.3 76.0 - - - +
399C VAL* 1.3 68.1 + - + +
401C GLU* 3.5 3.1 + - - +
402C ARG* 3.1 36.8 + - + +
324D GLN 5.0 1.9 + - - -
325D GLY* 4.6 12.3 + - - -
328D PRO* 4.8 21.5 + - - +
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Residues in contact with VAL 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ILE* 4.2 26.7 - - + +
380C ALA* 4.6 3.4 - - + -
381C ALA* 3.9 23.8 - - + +
384C VAL* 4.8 2.9 - - + -
395C ARG* 2.9 23.4 + - + +
396C LEU* 3.9 4.3 - - - +
398C THR* 1.3 79.2 - - + +
400C MET* 1.3 70.5 + - - +
402C ARG* 3.1 21.6 + - - +
403C LEU* 2.8 19.5 + - + +
430C LEU* 3.9 29.6 - - + +
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Residues in contact with MET 400 (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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345C LEU* 4.5 5.2 - - + -
352C LEU* 3.4 34.3 - - + -
353C THR* 3.9 22.9 - - + +
356C TYR* 3.3 46.7 - - + +
369C PHE* 4.0 10.1 - - + -
377C ILE* 4.0 31.6 - - + -
396C LEU 2.7 24.5 + - - +
397C HIS* 4.0 3.6 - - - +
399C VAL* 1.3 71.8 - - - +
401C GLU* 1.3 55.4 - - - +
403C LEU* 2.6 31.6 + - - +
404C MET* 2.8 14.2 + - + -
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Residues in contact with GLU 401 (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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356C TYR* 2.7 29.7 + - - +
397C HIS 3.2 17.0 + - - +
398C THR 4.1 2.9 - - - +
399C VAL 3.4 0.2 - - - -
400C MET* 1.3 78.9 - - - +
402C ARG* 1.3 60.6 + - - +
404C MET* 4.2 4.0 - - - +
405C ASP* 3.4 21.3 + - - +
408C SER* 4.3 19.6 + - - -
29D ILE* 4.7 6.6 - - - +
33D ASN* 4.8 4.8 + - - -
51D LYS* 3.2 33.0 - - + +
328D PRO* 4.4 12.3 - - + -
329D ILE* 3.9 30.5 - - + +
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Residues in contact with ARG 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C VAL* 5.5 8.3 - - - +
395C ARG* 5.9 0.2 - - - +
398C THR* 3.1 29.2 + - - +
399C VAL* 3.5 25.0 - - - +
400C MET 2.8 1.2 + - - -
401C GLU* 1.3 77.6 - - - +
403C LEU* 1.3 58.5 + - - +
405C ASP* 3.2 25.4 - - - +
406C LYS* 3.7 9.2 + - - +
429C ALA 4.1 5.9 - - - +
430C LEU* 4.0 44.8 + - + +
432C GLU 5.6 6.3 + - - -
433C VAL* 5.7 7.1 - - - +
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Residues in contact with LEU 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C PHE* 4.7 1.6 - - + -
377C ILE* 3.5 35.0 - - + -
399C VAL* 2.8 12.4 + - + +
400C MET* 2.6 16.2 + - - +
402C ARG* 1.3 70.8 - - - +
404C MET* 1.3 104.3 + - + +
405C ASP* 2.9 13.5 + - - +
406C LYS* 4.4 5.9 + - - +
407C ILE* 5.4 2.0 + - + +
421C ILE* 4.3 14.8 - - + -
425C TYR* 5.4 8.4 + - + -
426C VAL* 3.7 26.0 - - + -
429C ALA* 3.8 27.1 - - + +
430C LEU* 4.0 11.4 - - + +
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Residues in contact with MET 404 (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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356C TYR* 3.6 60.8 - - + +
360C MET* 4.1 17.5 - - + -
367C ILE* 3.5 23.8 - - + -
369C PHE* 4.2 3.8 - - - -
400C MET* 2.8 15.8 + - + +
401C GLU* 4.1 4.7 - - - +
403C LEU* 1.3 99.1 - - + +
405C ASP* 1.3 67.9 + - - +
406C LYS 3.7 0.7 - - - -
407C ILE* 4.2 13.2 - - + +
408C SER* 3.0 23.5 + - - -
421C ILE* 3.9 15.3 - - - -
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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