Contacts of the helix formed by residues 385 - 397 (chain C) in PDB entry 2AXT
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 GLN 385 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383C ASP* 3.3 22.1 + - - +
384C ILE* 1.3 77.2 - - - +
386C PRO* 1.3 76.7 - - + +
387C TRP* 3.1 36.3 - - + +
388C GLN* 3.1 23.5 + - - +
389C GLU* 3.4 3.8 + - - +
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Residues in contact with PRO 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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384C ILE 4.1 3.4 - - - +
385C GLN* 1.3 86.9 - - + +
387C TRP* 1.3 63.9 + - - +
388C GLN 2.8 7.1 + - - -
389C GLU* 2.9 22.8 + - + +
390C ARG* 3.1 30.3 + - - +
116V GLU* 3.8 29.8 - - + +
117V VAL* 4.2 12.1 - - + +
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Residues in contact with TRP 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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364C PRO* 4.4 7.9 - - + -
365C TRP* 3.7 26.0 - - + -
368C PRO* 5.1 6.7 - - + -
385C GLN* 3.1 40.2 - - + +
386C PRO* 1.3 78.2 - - + +
388C GLN* 1.3 76.2 + - + +
390C ARG* 3.6 31.0 + - - +
391C ARG* 3.0 57.3 + - - +
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Residues in contact with GLN 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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315C MET* 5.6 4.5 - - + -
319C ILE* 5.2 0.9 - - - -
365C TRP* 2.7 35.7 + - + +
368C PRO* 4.1 19.8 - - - +
369C LEU* 4.4 12.8 - - + +
383C ASP 3.9 4.2 + - - +
384C ILE* 3.6 17.8 - - + +
385C GLN* 3.3 25.1 + - - +
386C PRO 2.9 0.6 - - - -
387C TRP* 1.3 113.8 - - + +
389C GLU* 1.3 58.3 + - - +
390C ARG 3.1 1.8 - - - -
391C ARG* 4.1 4.0 - - - -
392C ALA* 2.7 38.1 + - - +
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Residues in contact with GLU 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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316C THR* 4.8 4.4 + - - +
319C ILE* 3.9 43.6 - - + +
320C ARG* 5.7 1.6 + - - -
323C LYS* 3.0 34.9 + - - +
384C ILE* 5.1 4.4 - - + +
385C GLN 3.4 4.1 + - - +
386C PRO* 2.9 16.6 + - + +
388C GLN* 1.3 79.7 - - - +
390C ARG* 1.3 55.9 + - - +
392C ALA* 3.9 3.3 - - - +
393C ALA* 3.3 22.2 + - - +
117V VAL* 3.7 29.4 - - + +
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Residues in contact with ARG 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C PRO* 3.1 27.4 + - - +
387C TRP* 3.6 28.3 + - - +
389C GLU* 1.3 74.4 - - - +
391C ARG* 1.3 65.5 + - - +
392C ALA 3.2 1.3 - - - -
393C ALA* 3.2 7.1 + - - +
394C GLU* 2.8 28.6 + - - +
116V GLU* 2.9 29.6 + - - +
117V VAL* 4.4 15.0 - - + +
126V ILE* 3.0 52.0 - - - +
127V PHE* 3.8 26.0 - - + -
552V HEM 5.4 2.6 - - + +
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Residues in contact with ARG 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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102C GLY* 5.5 4.9 + - - -
188C THR* 5.9 0.4 - - - +
300C GLU* 3.6 26.9 + - - +
364C PRO* 5.9 2.4 - - - +
365C TRP* 3.4 35.0 - - + +
387C TRP* 3.0 39.3 + - - +
388C GLN* 3.0 5.5 + - - +
390C ARG* 1.3 78.6 - - + +
392C ALA* 1.3 62.9 + - - +
394C GLU* 3.1 8.9 + - + +
395C TYR* 3.1 58.8 + - + -
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Residues in contact with ALA 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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312C ALA* 3.1 29.2 - - + +
315C MET* 3.6 34.8 - - + -
316C THR* 3.6 12.0 + - - +
365C TRP* 4.6 11.3 - - + -
388C GLN 2.7 21.9 + - - +
389C GLU* 3.9 5.8 - - - +
391C ARG* 1.3 74.0 - - - +
393C ALA* 1.3 61.4 + - - +
395C TYR* 4.9 0.4 - - - -
396C MET* 3.2 8.7 + - - +
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Residues in contact with ALA 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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316C THR* 3.8 12.3 + - + +
389C GLU 3.3 15.5 + - - +
390C ARG* 3.2 8.9 + - - +
391C ARG 3.2 0.6 - - - -
392C ALA* 1.3 78.8 - - - +
394C GLU* 1.3 65.5 + - - +
395C TYR 3.2 0.3 + - - -
396C MET* 3.3 5.7 + - - +
397C THR* 3.1 27.4 + - - +
74V THR* 4.2 16.4 - - + +
117V VAL* 6.4 0.9 - - + -
552V HEM 4.2 20.6 - - + -
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Residues in contact with GLU 394 (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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80C PRO* 4.1 4.6 - - - +
82C TYR* 2.6 29.7 + - - +
83C GLU* 3.6 8.1 - - - +
390C ARG 2.8 17.1 + - - +
391C ARG* 3.3 13.0 - - + +
393C ALA* 1.3 73.1 - - - +
395C TYR* 1.3 72.1 + - + +
397C THR* 2.9 10.4 + - - -
398C HIS* 2.8 52.7 + - - -
65V SER* 5.5 0.3 + - - -
127V PHE* 6.0 2.8 - - - -
552V HEM 5.4 6.5 - - - +
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Residues in contact with TYR 395 (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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82C TYR* 4.5 8.7 - + - -
299C SER* 3.9 23.3 + - - -
300C GLU* 4.3 7.1 - - - +
304C PRO* 3.5 23.2 - - + +
308C GLU* 3.6 38.1 - - + -
309C ALA* 3.7 11.9 - - - +
312C ALA* 4.1 9.6 - - + -
365C TRP* 3.6 24.4 - + - -
391C ARG* 3.1 44.6 + - + +
392C ALA 4.1 3.4 - - - +
394C GLU* 1.3 91.0 - - + +
396C MET* 1.3 66.1 + - - +
397C THR 3.0 1.6 - - - -
398C HIS* 3.0 13.5 + - + -
399C ALA 3.4 9.2 + - - -
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Residues in contact with MET 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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341A LEU* 3.3 49.5 - - + +
343A LEU* 4.2 8.2 - - + +
309C ALA* 4.1 12.6 - - - +
312C ALA* 4.1 1.0 - - - +
313C GLN* 3.7 45.3 - - + +
316C THR* 3.8 23.1 - - - +
317C PHE* 4.2 3.6 - - + -
392C ALA 3.2 14.3 + - - +
393C ALA 3.6 9.9 - - - +
395C TYR* 1.3 78.3 - - - +
397C THR* 1.3 64.5 + - + +
398C HIS 3.3 1.1 + - - -
399C ALA* 4.2 6.3 + - - +
73V LYS* 3.6 21.8 - - + +
74V THR* 3.9 14.1 - - + -
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Residues in contact with THR 397 (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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341A LEU* 5.6 1.3 - - - -
393C ALA 3.1 14.0 + - - +
394C GLU* 2.9 17.5 + - - -
396C MET* 1.3 81.3 - - + +
398C HIS* 1.3 76.5 + - - +
399C ALA 3.7 0.9 - - - -
419C PHE* 5.6 0.3 - - - -
65V SER* 3.7 33.5 + - - +
66V CYS* 4.4 9.4 - - + -
73V LYS* 4.4 10.3 - - + +
74V THR* 3.8 24.5 - - + -
552V HEM 5.4 3.5 - - + +
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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