Contacts of the helix formed by residues 351 - 363 (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 SER 351 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344C ILE 3.8 13.2 - - - -
345C LEU 3.1 11.7 + - - -
346C THR* 3.6 15.8 + - - -
348C PRO* 2.8 23.1 + - - -
350C ALA* 1.3 70.2 - - - +
352C LEU* 1.3 59.8 + - - +
353C THR* 3.1 11.3 + - - -
354C GLU* 3.1 24.9 + - - +
355C GLN* 2.9 32.4 + - - +
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Residues in contact with LEU 352 (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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344C ILE 4.6 3.1 + - - +
345C LEU* 3.9 13.3 + - + -
351C SER* 1.3 72.3 - - - +
353C THR* 1.3 67.9 + - - +
355C GLN* 2.9 23.8 + - + +
356C TYR* 2.8 31.9 + - + -
396C LEU* 3.5 35.4 - - + -
397C HIS* 3.7 31.4 - - + +
400C MET* 3.4 37.7 - - + -
51D LYS* 4.8 9.2 - - - +
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Residues in contact with THR 353 (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* 3.0 27.3 + - + +
346C THR* 3.5 19.5 - - + +
351C SER* 3.1 3.1 + - - -
352C LEU* 1.3 75.6 - - - +
354C GLU* 1.3 69.8 + - - +
355C GLN 3.0 1.0 + - - -
356C TYR 4.5 0.2 - - - +
357C LYS* 3.0 31.0 + - - +
369C PHE* 3.4 44.7 - - + -
374C VAL* 4.6 4.7 - - + -
377C ILE* 5.4 1.6 - - + -
400C MET* 3.9 14.1 - - + -
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Residues in contact with GLU 354 (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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346C THR 4.0 11.8 - - - +
347C GLU 4.4 3.6 - - - +
348C PRO 3.8 11.1 - - - +
349C HIS* 4.5 3.0 - - - -
350C ALA* 3.1 25.1 + - - -
351C SER* 3.1 20.1 + - - +
353C THR* 1.3 83.6 + - - +
355C GLN* 1.3 59.0 + - - +
357C LYS* 3.8 8.5 - - + +
358C ALA* 3.3 21.8 + - - +
44D LEU* 4.4 6.9 - - + +
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Residues in contact with GLN 355 (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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350C ALA 3.7 15.2 + - - +
351C SER 2.9 24.2 + - - +
352C LEU* 2.9 33.4 + - + +
354C GLU* 1.3 74.0 - - - +
356C TYR* 1.3 70.2 + - + +
357C LYS 3.2 1.1 - - - -
358C ALA* 3.0 7.5 + - - +
359C LEU* 2.7 32.8 + - + +
397C HIS* 5.2 4.9 - - - -
44D LEU* 4.3 15.3 - - + -
47D GLU* 4.7 7.0 + - - -
48D VAL* 3.1 40.6 - - + +
49D THR 4.5 0.7 + - - -
51D LYS* 5.4 4.4 + - - +
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Residues in contact with TYR 356 (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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352C LEU* 2.8 26.2 + - + +
353C THR 4.2 1.8 - - - +
355C GLN* 1.3 73.7 - - + +
357C LYS* 1.3 65.1 + - - +
359C LEU* 2.8 14.9 + - + -
360C MET* 2.7 35.7 + - + +
367C ILE* 4.6 0.4 - - + -
369C PHE* 4.4 6.7 - - + -
397C HIS 4.7 0.2 + - - -
400C MET* 3.3 47.0 - - + +
401C GLU* 2.7 43.0 + - - +
404C MET* 3.6 44.9 - - + -
408C SER* 5.5 5.8 - - - -
33D ASN* 6.1 2.7 - - - -
51D LYS* 4.0 15.9 + - - -
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Residues in contact with LYS 357 (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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353C THR* 3.0 20.9 + - - +
354C GLU* 3.8 7.4 - - - +
356C TYR* 1.3 79.0 - - - +
358C ALA* 1.3 63.8 + - - +
360C MET* 3.4 1.2 + - - +
361C ALA* 2.9 22.3 + - - +
365C VAL 4.8 0.2 - - - +
367C ILE* 3.1 42.7 - - + +
368C ALA* 3.5 5.8 - - - +
369C PHE* 3.4 43.3 + - + +
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Residues in contact with ALA 358 (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 GLU 3.3 7.4 + - - +
355C GLN 3.0 8.2 + - - +
357C LYS* 1.3 80.9 - - - +
359C LEU* 1.3 56.5 + - + +
361C ALA* 3.2 20.7 - - - +
362C THR* 3.3 4.3 + - - -
40D LEU* 3.1 23.9 - - + +
44D LEU* 3.4 31.6 - - + -
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Residues in contact with LEU 359 (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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355C GLN* 2.7 34.3 + - + +
356C TYR* 2.8 19.3 + - + +
358C ALA* 1.3 68.4 - - + +
360C MET* 1.3 78.7 + - + +
361C ALA 3.0 1.3 - - - -
362C THR* 2.8 23.4 + - - -
363C GLU 3.8 1.0 + - - -
33D ASN* 4.5 12.3 - - + +
36D ARG* 3.3 38.6 - - + +
37D ARG* 3.6 15.9 - - + +
40D LEU* 4.0 15.9 - - + -
44D LEU* 6.0 0.4 - - + -
48D VAL* 3.9 27.8 - - + -
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Residues in contact with MET 360 (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 25.7 + - + +
359C LEU* 1.3 85.3 - - + +
361C ALA* 1.3 63.5 + - - +
363C GLU* 2.9 17.8 + - - +
365C VAL* 3.1 32.5 + - + +
367C ILE* 4.1 15.3 - - + -
404C MET* 4.1 21.5 - - + -
407C ILE* 3.5 28.0 - - + -
408C SER* 4.2 9.9 - - - +
411C ALA* 3.6 11.7 - - + -
33D ASN* 4.9 0.7 - - - +
36D ARG* 3.2 33.0 - - - +
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Residues in contact with ALA 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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357C LYS 2.9 20.1 + - - +
358C ALA* 3.2 15.3 - - - +
360C MET* 1.3 75.1 - - - +
362C THR* 1.3 54.0 + - - +
364C GLY* 2.6 28.8 + - - -
365C VAL 3.2 12.0 + - - -
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Residues in contact with THR 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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358C ALA 3.3 10.0 + - - -
359C LEU* 2.8 17.9 + - - -
361C ALA* 1.3 76.4 - - - +
363C GLU* 1.3 59.6 + - - +
364C GLY* 3.1 1.0 + - - -
35D TRP* 3.7 25.1 - - + -
36D ARG* 3.9 19.4 + - - +
39D GLN* 3.2 41.5 - - + +
40D LEU* 4.1 3.5 - - - +
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Residues in contact with GLU 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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359C LEU 4.5 1.6 - - - +
360C MET* 2.9 12.0 + - - +
362C THR* 1.3 77.8 - - - +
364C GLY* 1.3 57.2 + - - +
365C VAL 3.3 2.5 - - - -
411C ALA* 3.3 28.9 - - + +
412C SER* 3.2 34.2 + - - +
415C ASN* 3.9 14.0 + - - +
32D ARG* 2.8 41.8 + - - +
35D TRP* 3.6 8.1 - - - -
36D ARG* 2.9 46.0 + - + +
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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