Contacts of the helix formed by residues 345 - 353 (chain C) in PDB entry 4H9Q
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 345 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B TYR* 4.6 0.9 + - - -
101B GLY 4.3 5.2 - - - +
343C ASP 3.3 10.0 + - - +
344C TYR* 1.3 88.9 - - - +
346C PRO* 1.3 77.8 - - + +
347C GLY* 4.4 7.3 - - - +
348C VAL* 3.1 49.3 + - + +
349C ASP 4.1 1.2 + - - -
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Residues in contact with PRO 346 (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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91B LYS* 4.7 7.4 - - - +
100B PHE 4.8 0.2 - - - +
101B GLY 4.1 12.3 - - - +
102B GLY* 4.6 13.0 - - - +
344C TYR* 3.4 32.3 - - + +
345C ARG* 1.3 87.8 - - + +
347C GLY* 1.3 60.6 + - - +
348C VAL 3.1 1.7 + - - -
349C ASP* 3.3 21.2 + - + +
352C LEU* 3.4 7.2 - - - +
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Residues in contact with GLY 347 (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 ARG* 3.1 8.6 + - - +
346C PRO* 1.3 79.7 - - - +
348C VAL* 1.3 62.4 - - - +
349C ASP 3.4 0.6 - - - +
352C LEU* 3.6 19.3 - - - +
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 3.8 15.7 - - - +
343C ASP 5.9 0.4 - - - +
345C ARG* 3.1 58.3 + - + +
347C GLY* 1.3 78.9 - - - +
349C ASP* 1.3 67.1 + - - +
350C PRO* 3.0 9.9 - - - +
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Residues in contact with ASP 349 (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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72B TYR* 2.7 22.3 + - - -
88B TYR* 3.6 22.2 - - + +
92B ARG* 3.0 27.4 + - - -
346C PRO* 3.3 17.1 + - + +
347C GLY 3.4 0.6 - - - +
348C VAL* 1.3 76.2 - - - +
350C PRO* 1.3 73.3 - - - +
351C ALA* 3.0 11.8 + - - -
352C LEU* 2.9 32.5 + - + +
353C SER* 4.4 1.4 + - - -
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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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72B TYR* 3.9 12.1 - - + -
75B HIS* 4.2 17.4 - - + +
88B TYR* 3.7 22.9 - - + +
348C VAL 3.0 9.6 - - - +
349C ASP* 1.3 89.7 - - - +
351C ALA* 1.3 60.3 + - - +
353C SER* 3.0 21.3 + - - +
354C ASP* 3.5 12.5 + - - +
357C LEU* 3.9 16.2 - - + -
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.8 0.4 - - - +
92B ARG* 3.4 29.2 - - - +
349C ASP* 3.0 9.1 + - - +
350C PRO* 1.3 77.8 - - - +
352C LEU* 1.3 62.0 + - - +
353C SER 3.1 1.1 + - - -
354C ASP 3.5 15.9 + - - +
357C LEU* 3.6 15.3 - - + +
358C ALA* 3.7 18.0 - - + +
361C LEU* 3.6 21.3 - - + -
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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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92B ARG* 5.5 3.8 - - - +
346C PRO 3.4 25.8 - - - +
347C GLY* 3.6 24.2 - - - +
349C ASP* 2.9 24.0 + - + +
351C ALA* 1.3 79.5 - - - +
353C SER* 1.3 59.3 + - - +
354C ASP 3.7 0.2 - - - -
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Residues in contact with SER 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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349C ASP 4.9 0.9 + - - -
350C PRO* 3.0 12.3 + - - +
352C LEU* 1.3 80.2 - - - +
354C ASP* 1.3 59.7 + - - +
355C PRO* 4.0 8.1 - - - +
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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