Contacts of the helix formed by residues 349 - 358 (chain C) in PDB entry 5H9U
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 ARG 349 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C ASP* 3.1 23.8 + - - -
123C LEU* 3.4 40.8 - - - +
124C ASP* 2.6 40.6 + - - -
318C ALA* 3.5 17.9 - - - +
319C ARG* 3.9 24.7 - - + +
320C PRO* 4.8 2.0 - - + -
347C ASP* 2.9 38.0 + - - +
348C PRO* 1.3 78.8 - - + +
350C PRO* 1.3 64.6 - - + +
351C LEU 3.4 0.9 - - - -
352C ALA* 2.9 8.5 + - + +
353C ILE* 2.8 32.6 + - - +
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Residues in contact with PRO 350 (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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123C LEU 5.2 0.2 - - - +
126C VAL* 3.6 34.3 - - + +
127C GLY 4.3 11.2 - - - +
128C ALA 4.4 0.9 - - - +
280C PRO 6.1 0.2 - - - +
281C THR* 5.3 5.8 - - - +
283C VAL* 3.8 29.4 - - + -
286C SER* 5.3 4.1 + - - +
313C TYR* 4.5 3.8 - - + -
318C ALA* 3.3 16.6 - - - +
348C PRO 3.7 2.2 - - - +
349C ARG* 1.3 85.4 - - + +
351C LEU* 1.3 57.1 + - - +
353C ILE* 3.2 12.1 + - + +
354C ILE* 3.0 39.3 + - + +
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Residues in contact with LEU 351 (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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122C PRO* 3.3 28.5 - - + +
123C LEU* 4.4 17.7 + - + +
125C ARG* 4.8 4.9 - - + -
126C VAL* 3.9 31.9 - - + +
349C ARG* 3.4 0.4 - - - +
350C PRO* 1.3 80.2 - - - +
352C ALA* 1.3 62.5 + - - +
354C ILE* 3.4 14.8 + - + +
355C GLU* 3.0 52.9 + - + +
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Residues in contact with ALA 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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123C LEU* 4.0 18.8 - - + +
347C ASP* 3.6 40.4 - - + +
349C ARG* 2.9 15.4 + - + +
351C LEU* 1.3 81.4 - - - +
353C ILE* 1.3 56.7 + - - +
355C GLU* 3.8 3.8 - - - +
356C GLU* 2.8 39.6 + - + +
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Residues in contact with ILE 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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283C VAL* 6.1 0.4 - - + -
286C SER* 3.7 31.0 - - - +
287C ALA* 4.0 13.5 - - + +
290C TYR* 3.6 49.8 - - + -
311C LEU* 5.5 0.2 - - + -
313C TYR* 3.9 8.1 - - + +
347C ASP 3.9 6.1 - - - +
348C PRO 3.4 21.8 - - - +
349C ARG 2.8 16.3 + - - +
350C PRO* 3.5 10.8 - - + +
352C ALA* 1.3 73.4 - - - +
354C ILE* 1.3 66.7 - - - +
356C GLU 3.2 0.5 + - - -
357C LEU* 3.0 32.4 + - + +
359C LEU* 4.2 2.4 - - + +
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Residues in contact with ILE 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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126C VAL* 6.3 2.2 - - + -
280C PRO* 3.8 28.3 - - + +
281C THR* 3.8 31.9 - - + -
286C SER* 5.1 1.3 - - - -
350C PRO* 3.0 26.0 + - + +
351C LEU* 3.8 14.6 - - + +
353C ILE* 1.3 76.0 - - - +
355C GLU* 1.3 62.9 + - + +
358C ASP* 2.9 28.4 + - - -
359C LEU* 3.3 13.7 + - + +
360C LEU* 3.6 37.0 - - + -
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Residues in contact with GLU 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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123C LEU* 4.1 14.8 - - - +
351C LEU* 3.0 45.7 + - + +
352C ALA* 4.0 3.2 - - - +
354C ILE* 1.3 80.7 - - + +
356C GLU* 1.3 64.9 + - + +
357C LEU 3.4 0.3 + - - -
358C ASP* 3.5 10.9 + - - +
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Residues in contact with GLU 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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290C TYR* 2.7 39.6 + - + -
293C TYR* 4.4 11.6 + - + +
346C PHE* 5.1 2.6 - - - -
347C ASP* 3.6 22.4 + - - +
352C ALA* 2.8 30.3 + - + +
353C ILE 3.9 3.1 - - - +
355C GLU* 1.3 74.1 - - + +
357C LEU* 1.3 65.6 + - + +
385C ARG* 5.5 7.6 + - - -
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Residues in contact with LEU 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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289C TYR* 4.7 1.6 - - + -
290C TYR* 3.9 30.5 - - + +
293C TYR* 4.1 27.8 - - + -
353C ILE* 3.0 19.7 + - + +
356C GLU* 1.3 82.9 - - - +
358C ASP* 1.3 72.3 + - - +
359C LEU* 3.4 28.9 + - + -
361C ARG* 4.0 1.7 + - - -
379C PRO* 3.5 46.3 - - + +
380C TRP* 4.3 17.3 - - + -
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Residues in contact with ASP 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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37C LYS* 4.8 5.4 + - - -
354C ILE 2.9 11.7 + - - -
355C GLU* 3.5 10.0 + - - +
356C GLU 5.5 0.2 - - - +
357C LEU* 1.3 79.2 - - - +
359C LEU* 1.3 59.4 + - - +
360C LEU* 3.1 17.4 + - - +
361C ARG* 2.9 46.5 + - - +
363C ILE* 5.2 0.2 - - - +
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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