Contacts of the helix formed by residues 353 - 359 (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 GLY 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A ALA 4.5 6.1 - - - -
338A ASN* 3.9 27.5 - - - +
339A PHE* 4.9 3.4 - - - -
342C MET* 3.3 10.9 - - - +
352C GLY* 1.3 70.1 - - - -
354C GLU* 1.3 64.9 + - - -
355C THR* 2.7 8.8 + - - -
356C MET* 2.8 26.8 + - - +
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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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87A ASN* 3.4 17.7 + - - +
333A GLU* 3.3 4.1 - - - +
336A ALA* 3.8 26.9 + - + +
337A HIS* 3.2 21.9 + - + +
342A ASP* 3.2 3.5 - - - +
343A LEU 5.4 0.2 + - - -
344A ALA* 2.4 34.2 + - + +
565A OEC 2.1 43.1 + - - -
353C GLY* 1.3 70.8 - - - -
355C THR* 1.3 57.9 + - - +
356C MET* 2.7 8.8 + - - -
357C ARG* 3.2 28.0 + - - +
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Residues in contact with THR 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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339A PHE* 5.1 4.7 - - - -
310C SER* 3.1 45.6 + - - +
311C GLN* 2.8 33.0 - - - +
314C ALA* 4.7 4.4 - - + +
351C PHE* 4.2 11.2 - - + +
352C GLY 3.4 17.9 + - - -
353C GLY* 2.7 2.0 + - - -
354C GLU* 1.3 73.2 + - - +
356C MET* 1.3 60.1 + - - +
357C ARG 2.8 6.3 - - - +
358C PHE* 2.9 24.5 + - + -
359C TRP* 3.7 5.2 + - - +
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Residues in contact with MET 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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62A GLY* 3.3 44.9 - - - +
63A ILE* 4.2 3.4 - - + +
87A ASN* 3.2 22.8 - - - +
88A ALA* 4.1 21.7 - - - +
337C LEU* 3.8 10.3 - - + -
342C MET* 3.6 42.4 - - + +
350C ILE* 3.8 15.8 - - + +
351C PHE 4.0 2.6 + - - -
353C GLY* 2.8 17.8 + - - +
354C GLU* 2.7 1.6 + - - -
355C THR* 1.3 77.6 - - - +
357C ARG* 1.3 56.2 + - - +
359C TRP* 3.3 26.5 - - - +
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Residues in contact with ARG 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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87A ASN* 2.5 46.8 + - - +
88A ALA 5.6 0.4 - - - -
89A ILE 5.9 0.2 - - - -
90A GLY* 4.5 5.8 - - - -
91A LEU 5.4 0.9 + - - -
92A HIS* 5.6 1.9 - - - -
165A GLN* 2.8 24.4 + - - +
166A GLY 4.1 18.1 - - - +
167A SER* 3.9 8.3 - - - -
169A SER* 3.5 6.9 + - - -
170A ASP* 3.1 31.7 + - - -
344A ALA* 3.6 19.0 + - - -
565A OEC 4.3 1.2 + - - -
354C GLU* 3.2 30.4 + - - +
355C THR 2.8 0.6 - - - -
356C MET* 1.3 80.9 - - - +
358C PHE* 1.3 92.9 + - + +
359C TRP* 3.3 7.5 + - - -
360C ASP* 3.9 12.1 - - - +
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Residues in contact with PHE 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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164A GLY 5.4 1.1 - - - -
165A GLN 3.4 27.6 - - - -
166A GLY* 3.8 11.0 - - - -
343A LEU 3.9 2.7 - - - -
344A ALA* 3.5 19.3 - - + -
292C PHE* 6.3 0.2 - + - -
306C GLY 5.1 1.3 - - - -
307C PRO* 3.4 47.1 - - + +
310C SER* 3.3 40.2 - - - -
311C GLN* 3.7 12.3 - - - +
355C THR* 2.9 13.6 + - + +
357C ARG* 1.3 97.5 - - + +
359C TRP* 1.3 51.9 + - - +
360C ASP* 2.7 18.3 + - - +
361C PHE* 3.0 18.3 + - - +
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Residues in contact with TRP 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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88A ALA 4.6 6.4 + - - -
92A HIS* 3.6 35.0 + + - -
311C GLN* 4.6 8.5 - - - +
344C SER* 3.6 21.4 - - - -
345C PRO* 4.3 10.8 - - + +
346C THR* 3.6 15.5 - - + -
348C GLU* 3.3 30.3 - - + -
350C ILE* 3.5 44.5 - - + +
351C PHE 5.7 0.4 - - - +
355C THR 3.7 3.0 + - - +
356C MET 3.3 19.3 - - - +
357C ARG* 3.3 4.7 - - - -
358C PHE* 1.3 75.1 - - - +
360C ASP* 1.3 67.5 + - - +
361C PHE 3.5 3.2 - - - +
362C ARG* 5.5 1.4 - - - -
370C ARG* 5.4 3.1 + - - -
33O TYR* 3.4 27.3 + - - -
37O VAL* 4.2 12.6 - - + -
38O GLY* 4.8 1.1 - - - -
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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